Contacts of the helix formed by residues 298 - 319 (chain B) in PDB entry 2WWR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ARG* 3.7 24.0 - - - +
147A CYS* 3.9 4.7 - - - -
148A GLY 3.3 18.8 - - - +
150A GLY* 4.1 19.7 - - - +
110B THR* 3.7 15.8 + - + +
113B GLU* 4.3 0.4 - - - +
296B SER 3.2 2.4 + - - -
297B ALA* 1.3 81.7 - - - +
299B HIS* 1.3 65.1 + - - +
300B ARG* 4.0 4.6 + - - +
301B THR* 3.2 27.2 + - - -
302B ARG* 3.0 24.9 + - - +
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 6.1 0.9 - - - -
144A LEU 5.7 2.0 - - - -
147A CYS* 3.7 29.8 + - + +
148A GLY 3.5 11.4 + - - -
149A TYR* 3.4 44.6 + + + -
298B THR* 1.3 74.0 - - - +
300B ARG* 1.3 64.4 + - - +
302B ARG* 3.9 2.7 - - - +
303B ASN* 3.1 39.7 + - - +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A THR* 2.9 16.1 + - - -
153A GLN* 2.8 50.1 + - - +
154A SER* 5.4 2.7 - - - +
210A ASP* 5.4 4.2 + - - -
298B THR* 3.4 4.6 + - - +
299B HIS* 1.3 80.1 - - - +
301B THR* 1.3 56.9 + - - +
303B ASN* 4.0 4.0 - - - +
304B THR* 2.6 34.5 + - - -
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 3.9 9.7 + - + +
107B LEU* 3.7 36.3 - - + -
110B THR* 2.6 27.6 + - - +
296B SER* 4.0 16.8 - - - +
298B THR* 3.2 15.0 + - - -
300B ARG* 1.3 75.8 - - - +
302B ARG* 1.3 66.3 + - - +
304B THR* 3.1 7.8 + - - -
305B MET* 2.9 29.1 + - + +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 3.3 34.5 - - - +
142A LYS 3.0 25.3 + - - -
143A PRO* 3.1 32.9 + - - +
144A LEU* 5.8 1.1 - - + -
145A TRP 4.3 2.0 + - - -
147A CYS* 3.8 11.2 - - - -
16B PRO* 3.5 19.0 - - + +
81B MET* 4.5 3.4 - - - +
293B HIS 4.4 6.5 + - - -
296B SER* 2.9 50.5 + - - +
297B ALA* 3.4 18.2 - - - +
298B THR 3.0 20.8 + - - +
299B HIS* 4.0 2.7 - - - +
301B THR* 1.3 76.1 - - - +
303B ASN* 1.3 58.2 + - - +
305B MET* 3.6 10.7 + - - +
306B SER 3.2 20.3 + - - -
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Residues in contact with ASN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 6.0 1.8 - - - +
16B PRO* 3.5 19.9 - - - +
17B ALA* 3.5 15.6 + - - +
18B GLU* 3.6 32.8 + - - +
299B HIS* 3.1 35.6 + - - +
300B ARG* 4.0 4.7 - - - +
302B ARG* 1.3 75.7 - - - +
304B THR* 1.3 58.7 + - - +
306B SER* 3.2 7.1 - - - -
307B LEU* 3.0 27.9 + - - +
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 4.4 6.6 + - - -
106B VAL* 3.5 35.0 - - + -
300B ARG* 2.6 21.4 + - - +
301B THR* 3.1 8.8 + - - -
303B ASN* 1.3 73.8 - - - +
305B MET* 1.3 54.3 + - - +
307B LEU* 3.1 7.8 + - + +
308B LEU* 2.8 37.7 + - + +
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Residues in contact with MET 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 4.4 13.2 - - + -
81B MET* 3.5 36.6 - - + +
82B SER* 4.2 2.7 - - - -
103B THR* 3.8 30.5 - - + +
106B VAL* 4.0 15.0 - - + -
107B LEU* 3.8 16.8 - - + -
296B SER* 3.7 22.7 - - - +
301B THR* 2.9 30.5 + - + +
302B ARG* 3.7 15.5 - - - +
304B THR* 1.3 74.6 - - - +
306B SER* 1.3 57.0 + - - +
308B LEU* 3.4 2.8 + - - +
309B ALA* 2.9 31.9 + - - +
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Residues in contact with SER 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.6 8.8 - - - +
16B PRO* 2.9 42.8 + - - +
19B GLY* 3.0 18.0 - - - -
81B MET* 4.0 10.9 - - - +
302B ARG 3.2 12.4 + - - -
303B ASN* 3.2 10.8 - - - -
305B MET* 1.3 78.8 - - - +
307B LEU* 1.3 56.3 + - - +
309B ALA* 3.2 4.6 + - - +
310B ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.4 41.3 - - + +
19B GLY* 4.1 6.1 - - - -
22B ALA* 4.1 15.3 - - + -
303B ASN 3.0 12.7 + - - +
304B THR* 3.1 7.6 + - + +
306B SER* 1.3 76.8 - - - +
308B LEU* 1.3 59.1 + - - +
310B ALA* 3.8 1.1 - - - +
311B ASN* 3.0 53.7 + - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B THR* 4.0 24.9 - - + -
104B PRO 4.4 4.0 - - - +
106B VAL* 3.9 27.4 - - + -
304B THR* 2.8 17.8 + - + +
305B MET 3.8 4.5 - - - +
307B LEU* 1.3 76.0 - - - +
309B ALA* 1.3 60.2 + - - +
311B ASN* 3.5 3.5 + - + +
312B ASN* 2.9 39.8 + - - +
323B PRO* 3.5 31.6 - - + -
324B SER* 3.8 24.0 - - - +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 6.1 0.2 - - + -
56B LEU* 4.0 19.2 - - + +
79B SER* 2.6 29.3 + - - +
80B THR 4.2 12.1 - - - +
81B MET* 4.1 16.8 - - + -
103B THR* 4.5 1.7 - - + +
305B MET 2.9 17.9 + - - +
306B SER* 3.5 4.7 - - - +
308B LEU* 1.3 77.6 - - - +
310B ALA* 1.3 61.6 + - - +
312B ASN* 3.5 3.7 + - - +
313B LEU* 3.1 14.2 + - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY* 3.6 25.8 - - - +
22B ALA* 4.0 15.5 - - + -
23B LEU* 4.0 13.2 - - + +
56B LEU* 4.0 11.6 - - + +
306B SER 2.9 16.1 + - - +
307B LEU 3.8 4.9 - - - +
309B ALA* 1.3 76.5 - - - +
311B ASN* 1.3 57.2 + - - +
313B LEU* 3.4 4.0 + - - +
314B LEU* 3.0 32.9 + - - +
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Residues in contact with ASN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA* 4.6 3.8 - - - +
307B LEU* 3.0 46.0 + - - +
308B LEU* 4.0 4.6 - - - +
310B ALA* 1.3 73.3 - - - +
312B ASN* 1.3 60.2 + - - +
314B LEU* 3.8 16.8 - - - +
315B ALA* 2.9 31.0 + - - +
323B PRO* 4.0 18.9 - - + +
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Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 4.2 1.1 - - - +
79B SER* 3.6 14.5 + - - +
101B GLY* 3.9 1.5 - - - -
102B TYR 3.4 33.1 + - - +
308B LEU* 2.9 26.9 + - - +
309B ALA* 4.6 1.6 - - - +
310B ALA 3.3 0.2 - - - -
311B ASN* 1.3 75.0 - - - +
313B LEU* 1.3 57.8 + - - +
315B ALA 3.3 0.7 + - - -
316B GLY* 3.0 26.7 + - - -
322B MET* 3.6 29.6 - - + +
323B PRO* 3.0 26.4 - - - +
324B SER* 3.2 21.6 + - - -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.4 28.9 - - + -
23B LEU* 3.9 19.7 - - + -
54B GLY* 3.7 12.1 - - - -
55B LEU 3.5 39.3 - - - +
56B LEU* 3.9 18.6 - - + -
77B VAL* 3.6 15.3 - - + +
79B SER* 3.8 9.6 + - - -
309B ALA 3.1 9.8 + - - +
310B ALA 3.5 6.7 - - - +
312B ASN* 1.3 78.4 - - - +
314B LEU* 1.3 62.9 + - + +
316B GLY 3.2 1.6 + - - -
317B LEU* 2.9 34.9 + - + +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA* 4.3 15.9 - - + +
23B LEU* 4.2 14.6 - - + -
26B ALA* 3.9 29.2 - - + +
28B ASP* 4.6 0.2 - - - +
29B CYS* 4.2 22.9 - - - -
310B ALA 3.0 20.7 + - - +
311B ASN* 3.8 19.7 - - - +
313B LEU* 1.3 76.1 - - - +
315B ALA* 1.3 55.7 + - - +
317B LEU* 3.3 6.4 + - + +
318B ARG* 2.9 65.6 + - + +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ASN 2.9 19.7 + - - +
312B ASN 3.7 3.8 - - - +
314B LEU* 1.3 75.6 - - - +
316B GLY* 1.3 56.9 + - - +
318B ARG 3.4 0.9 + - - -
319B GLY 3.0 8.5 + - - -
320B GLU* 2.8 49.0 + - + +
321B PRO 3.9 17.7 - - - +
322B MET* 3.7 17.9 - - + -
323B PRO* 4.2 3.4 - - + -
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 3.6 13.2 - - - +
77B VAL* 4.0 21.3 - - - +
99B ARG* 3.7 23.9 + - - -
312B ASN 3.0 14.3 + - - -
313B LEU 3.2 3.1 + - - -
315B ALA* 1.3 73.6 - - - +
317B LEU* 1.3 65.1 + - - +
319B GLY* 3.3 10.6 + - - -
322B MET* 4.1 3.0 - - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B MET* 3.7 27.7 - - + +
9B VAL* 3.7 15.9 - - + -
29B CYS* 3.7 29.8 - - - -
53B HIS* 3.5 46.2 - - + +
54B GLY 3.7 2.7 - - - +
76B LYS* 3.2 29.3 + - + +
77B VAL* 3.8 8.2 - - + +
313B LEU* 2.9 29.0 + - + +
314B LEU* 3.7 8.5 - - + +
316B GLY* 1.3 74.6 - - - +
318B ARG* 1.3 62.8 + - + +
319B GLY 3.1 0.2 - - - -
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 4.8 6.1 - - + -
26B ALA* 3.1 30.1 - - - +
28B ASP* 2.7 36.0 + - - +
76B LYS* 5.4 0.4 - - - -
314B LEU* 2.9 47.2 + - - +
317B LEU* 1.3 77.8 - - + +
319B GLY* 1.3 60.5 + - - +
320B GLU* 3.7 32.1 + - + +
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 5.3 4.0 - - - -
99B ARG* 4.1 8.1 - - - -
315B ALA 3.0 4.7 + - - -
316B GLY 3.3 8.0 + - - -
317B LEU 3.1 5.8 + - - -
318B ARG* 1.3 79.9 - - - +
320B GLU* 1.3 60.1 + - - +
321B PRO* 4.9 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il