Contacts of the helix formed by residues 304 - 321 (chain A) in PDB entry 3P9K
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 ASN 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A PRO* 6.0 0.2 - - - +
302A GLU* 3.3 29.9 + - - +
303A ALA* 1.3 74.5 - - - +
305A PRO* 1.3 77.1 - - + +
306A SER* 2.7 36.3 + - - -
307A SER* 2.9 15.3 + - - +
308A GLN* 3.0 32.9 + - - +
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Residues in contact with PRO 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ASN* 1.3 89.0 - - + +
306A SER* 1.3 56.0 + - - +
308A GLN* 3.4 9.8 - - + +
309A GLY* 3.1 23.4 + - - -
352A ASN* 4.5 1.7 + - - -
15B ASP 5.7 0.9 - - - +
18B MET* 4.5 21.9 - - + +
19B PHE* 4.7 14.8 - - + +
22B GLN* 3.5 29.2 - - - +
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Residues in contact with SER 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASN* 2.7 22.7 + - - -
305A PRO* 1.3 73.1 - - - +
307A SER* 1.3 61.7 + - - -
309A GLY 3.4 0.3 + - - -
310A VAL* 3.2 14.2 + - - +
352A ASN* 2.8 44.2 + - - +
18B MET* 4.1 23.1 - - - +
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO* 4.2 12.1 - - - -
301A PRO* 4.1 15.5 - - - -
302A GLU 3.0 26.1 + - - -
303A ALA* 4.0 2.8 - - - -
304A ASN* 2.9 19.8 + - - -
306A SER* 1.3 68.5 - - - +
308A GLN* 1.3 77.5 + - - +
310A VAL* 2.8 17.0 + - - +
311A PHE* 3.0 33.7 + - - -
83B SER* 4.7 1.2 - - - -
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 4.9 2.2 - - - +
304A ASN* 3.0 32.0 + - - +
305A PRO* 3.4 3.3 - - - +
307A SER* 1.3 82.6 + - - +
309A GLY* 1.3 58.2 + - - +
311A PHE* 3.1 11.2 + - - +
312A HIS* 2.9 35.5 + - - -
22B GLN* 3.1 23.8 + - - +
83B SER* 2.9 40.4 + - - +
84B TYR* 3.0 38.0 - - + +
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Residues in contact with GLY 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A PRO 3.1 20.9 + - - -
306A SER 3.8 1.3 - - - -
307A SER 3.0 1.4 + - - -
308A GLN* 1.3 77.4 - - - +
310A VAL* 1.3 61.1 + - - +
312A HIS* 3.4 17.6 + - - +
313A VAL* 3.3 22.1 + - - +
352A ASN* 4.6 6.3 - - - -
18B MET 6.0 0.2 - - - -
21B LEU* 6.0 1.6 - - - -
22B GLN* 4.8 11.4 - - - +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A CYS* 4.1 23.8 - - + -
296A ILE 4.2 9.0 - - - +
297A LEU* 3.7 36.6 - - + +
298A PRO* 4.5 6.5 - - + -
306A SER 3.2 16.4 - - - +
307A SER* 2.8 12.6 + - - +
309A GLY* 1.3 73.2 - - - +
311A PHE* 1.3 60.7 + - + +
313A VAL* 3.5 5.6 + - - +
314A ASP* 3.2 16.1 + - - +
326A GLU* 3.5 11.6 - - + +
352A ASN* 3.7 24.9 - - + +
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 4.0 17.9 - - + -
298A PRO* 4.3 12.3 - - + -
301A PRO* 4.1 23.1 - - + -
307A SER* 3.0 34.3 + - - -
308A GLN 3.1 4.0 + - - +
310A VAL* 1.3 77.1 - - - +
312A HIS* 1.3 67.3 + - - +
314A ASP* 3.2 6.7 + - - +
315A MET* 3.0 26.5 + - - +
328A TYR* 5.4 0.4 - - - -
76B ARG 5.9 0.2 - - - +
79B ARG* 3.6 48.5 - - + -
80B LEU* 3.8 21.3 - - + +
83B SER* 3.5 30.3 - - - -
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Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLN 2.9 27.2 + - - -
309A GLY* 3.4 8.9 - - - +
311A PHE* 1.3 76.5 - - - +
313A VAL* 1.3 57.2 + - + +
315A MET* 3.2 4.7 + - - +
316A ILE* 2.9 31.9 + - - +
22B GLN* 3.5 31.8 + - + +
25B SER* 3.1 39.3 + - - +
26B SER* 4.3 7.4 - - - -
28B VAL* 3.7 19.1 - - + +
29B LEU* 5.2 2.5 + - + +
80B LEU* 3.7 16.2 - - + -
84B TYR* 2.5 36.5 + + - -
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A TRP* 4.9 8.7 - - + +
266A HIS* 4.0 18.2 - - + -
295A CYS* 5.0 10.5 - - - -
309A GLY 3.3 16.8 - - - +
310A VAL* 3.8 7.2 - - - +
311A PHE 3.2 0.4 - - - -
312A HIS* 1.3 75.3 - - + +
314A ASP* 1.3 59.5 + - - +
316A ILE* 3.2 7.5 + - + +
317A MET* 2.8 39.6 + - + +
326A GLU* 3.0 28.0 - - - +
601A CIY 4.3 27.4 - - + +
25B SER* 5.4 1.3 - - - +
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 4.9 1.1 - - + -
310A VAL 3.2 8.6 + - - +
311A PHE* 3.2 13.8 + - - +
313A VAL* 1.3 77.8 - - - +
315A MET* 1.3 57.5 + - - +
317A MET* 3.1 3.1 + - - +
318A LEU 2.9 12.1 + - - -
325A ARG* 3.7 1.6 - - - +
326A GLU* 3.0 38.7 + - + +
76B ARG* 2.9 66.5 + - - +
79B ARG* 2.7 32.4 + - - +
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Residues in contact with MET 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 3.8 11.7 - - + -
140A LEU* 3.8 26.2 - - + -
311A PHE 3.0 15.0 + - - +
312A HIS 3.5 7.6 - - - +
314A ASP* 1.3 75.1 - - - +
316A ILE* 1.3 64.9 + - - +
318A LEU* 3.0 21.3 + - + +
319A ALA* 2.8 24.6 + - - +
28B VAL* 3.7 13.9 - - + -
32B THR* 3.6 17.0 - - + +
76B ARG* 3.8 29.8 - - - +
77B ILE* 3.9 14.6 - - + -
80B LEU* 3.9 24.5 - - + -
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASN* 3.5 17.9 - - - +
137A TRP* 4.6 6.5 - - + -
312A HIS 2.9 19.0 + - - +
313A VAL* 3.4 12.3 - - - +
315A MET* 1.3 75.6 - - - +
317A MET* 1.3 78.5 + - + +
319A ALA* 3.3 3.5 + - - -
320A HIS* 3.1 45.4 + - + +
601A CIY 3.5 42.4 - - + +
25B SER* 3.7 18.2 - - - +
28B VAL* 3.8 11.9 - - + -
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Residues in contact with MET 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A HIS* 3.2 31.0 - - + +
267A ASP* 3.4 9.2 - - - +
313A VAL* 2.8 20.3 + - + +
314A ASP* 3.3 7.9 - - - +
316A ILE* 1.3 92.2 - - + +
318A LEU* 1.3 64.9 + - - +
321A ASN* 3.0 59.0 + - - +
324A GLY* 3.5 21.2 - - - +
325A ARG* 3.8 4.3 - - - +
326A GLU* 3.7 13.2 - - - +
601A CIY 3.6 27.6 - - + -
76B ARG* 4.0 0.7 - - - +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 4.1 20.0 - - + -
143A ALA* 6.3 0.2 - - + -
149A ILE* 4.5 0.3 - - - +
150A PRO* 3.4 18.8 - - + +
314A ASP 2.9 8.6 + - - +
315A MET* 3.0 35.2 + - + +
317A MET* 1.3 79.3 - - - +
319A ALA* 1.3 63.0 + - - +
320A HIS 3.5 0.2 + - - -
321A ASN 4.4 6.0 - - - +
324A GLY 4.4 0.9 - - - -
73B MET* 4.2 52.9 - - + +
76B ARG* 3.7 34.1 - - + +
77B ILE* 4.5 2.2 - - + -
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 3.6 8.1 - - - -
137A TRP* 4.0 27.4 - - + -
140A LEU* 5.5 2.2 - - + -
150A PRO* 3.3 16.4 - - + +
151A PHE 3.0 24.8 + - - -
315A MET 2.8 14.8 + - - +
316A ILE 3.3 4.7 + - - +
318A LEU* 1.3 79.1 - - - +
320A HIS* 1.3 78.3 + - + +
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Residues in contact with HIS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASN* 5.3 1.4 + - - -
133A LEU* 3.3 51.1 - - + +
136A SER* 2.8 34.1 + - - -
137A TRP* 4.7 7.9 + - - -
149A ILE* 3.5 13.8 - - - +
151A PHE* 3.6 21.1 - - + +
152A ASN* 4.2 3.6 - - - +
159A ALA* 3.8 15.4 + - + +
316A ILE* 3.1 40.0 + - + +
319A ALA* 1.3 88.5 - - + +
321A ASN* 1.3 71.5 + - - +
322A PRO* 4.3 1.0 - - - +
601A CIY 5.2 6.5 - + + -
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 3.7 14.2 - - - +
159A ALA* 4.2 10.4 - - - +
160A PHE* 4.2 11.1 - - - -
267A ASP* 3.2 30.2 + - - +
317A MET* 3.0 56.3 + - - +
318A LEU* 4.4 2.8 - - - +
320A HIS* 1.3 87.1 - - - +
322A PRO* 1.4 65.5 - - + +
323A GLY* 2.8 15.5 + - - -
324A GLY* 3.6 2.8 + - - +
601A CIY 3.4 14.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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