Contacts of the strand formed by residues 304 - 324 (chain B) in PDB entry 5U2H
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 VAL 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLN* 4.7 13.2 - - - +
300B LYS* 3.3 5.7 - - - +
301B GLU* 2.9 36.4 + - - +
302B ASN* 4.1 4.7 - - + +
303B ASN* 1.3 78.5 - - - +
305B GLU* 1.3 65.3 + - - +
306B LYS* 3.4 3.4 + - + +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 3.8 19.2 - - - +
116B GLN 4.7 2.6 + - - -
167B TRP* 5.6 10.3 - - + -
298B TYR* 4.5 20.4 - - + +
299B TYR 4.4 3.4 - - - -
300B LYS* 4.4 12.8 - - - +
303B ASN 4.4 0.2 - - - -
304B VAL* 1.3 72.9 - - - +
306B LYS* 1.3 66.4 + - - +
404B 7S1 5.3 11.0 - - + -
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY* 5.1 4.3 - - - +
114B GLN 3.4 12.1 - - - +
115B GLN* 4.7 3.6 - - + +
167B TRP* 5.8 2.0 - - - -
298B TYR* 3.4 7.6 - - - +
299B TYR* 2.9 61.9 + - + +
301B GLU* 5.2 2.9 - - + +
304B VAL* 4.3 4.7 - - + +
305B GLU* 1.3 79.0 - - - +
307B ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY 4.1 0.5 + - - -
114B GLN* 2.9 43.3 + - + +
167B TRP* 4.7 21.5 - - + -
296B ALA* 5.0 4.7 - - + -
297B LYS 3.6 7.2 - - - +
298B TYR* 3.6 27.8 - - + -
299B TYR* 4.5 2.7 - - - +
306B LYS* 1.3 75.1 - - - +
308B THR* 1.3 64.3 + - - +
309B LEU* 4.0 0.4 - - + -
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LYS* 4.4 6.3 - - - -
111B THR 3.5 12.6 - - - +
112B GLU* 4.0 22.1 - - + +
295B TYR 3.9 0.3 - - - +
296B ALA* 3.0 8.8 - - - -
297B LYS* 2.9 46.3 + - + +
299B TYR* 2.9 31.9 + - - -
307B ARG* 1.3 71.6 + - - +
309B LEU* 1.3 61.0 + - - +
310B ILE* 3.8 24.5 + - + +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE 4.0 0.9 - - - +
111B THR* 2.9 38.8 + - - +
114B GLN* 3.1 35.8 + - - +
167B TRP* 5.3 8.7 - - + -
171B GLU* 3.9 34.1 - - + +
294B ARG* 4.3 23.3 - - + -
295B TYR 4.4 1.8 - - - +
296B ALA* 4.2 16.8 - - + -
307B ARG* 4.0 2.0 + - + -
308B THR* 1.3 72.3 - - - +
310B ILE* 1.3 63.3 + - - +
311B LYS 4.3 0.4 - - - +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B MET* 5.2 4.0 - - + -
108B PHE* 4.3 13.9 - - + -
109B ILE 3.4 7.4 - - - +
110B LYS* 3.6 37.9 - - + -
294B ARG* 3.6 2.1 - - - -
295B TYR* 2.9 46.9 + - + +
297B LYS* 6.3 2.7 - - + -
308B THR* 4.0 11.7 - - + +
309B LEU* 1.3 81.1 - - - +
311B LYS* 1.3 67.5 - - - +
312B VAL* 3.7 21.5 + - + +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.1 7.6 - - - +
109B ILE* 2.9 52.2 + - + +
171B GLU* 4.4 16.2 + - - +
292B ASN* 5.6 3.6 - - - +
293B PHE 3.9 4.9 - - - +
294B ARG* 4.7 4.3 - - + +
309B LEU* 5.4 0.2 - - - +
310B ILE* 1.3 70.9 - - - +
312B VAL* 1.3 60.1 + - - +
313B PHE* 3.5 17.2 - - + -
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.5 34.3 - - + -
105B MET* 3.7 30.5 - - + -
107B ASN 4.0 2.2 - - - -
108B PHE* 4.7 0.7 - - + +
292B ASN* 2.9 27.6 - - - +
293B PHE* 2.9 39.8 + - + +
295B TYR* 4.5 9.4 - - + -
310B ILE* 3.8 23.6 - - + +
311B LYS* 1.3 75.6 - - - +
313B PHE* 1.3 62.7 + - - +
314B GLY 4.3 0.2 + - - -
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 4.3 1.8 - - - -
105B MET* 4.1 1.0 - - - -
106B THR* 3.0 5.8 + - - -
107B ASN* 2.8 63.0 + - + +
108B PHE* 3.9 0.9 - - - -
109B ILE* 3.8 34.5 - - + -
174B LYS 5.2 1.6 - - - -
175B ASP 5.2 0.2 - - - -
176B ALA* 4.6 23.3 - - + -
177B PRO* 5.1 0.2 - - + -
246B ALA 4.7 0.4 - - - +
247B ILE 4.4 2.9 - - - +
248B GLN* 4.1 24.7 - - - +
249B GLY* 4.5 0.4 - - - +
291B TYR 3.6 5.6 - - - +
292B ASN* 3.4 35.9 - - + -
311B LYS* 3.5 26.9 - - + -
312B VAL* 1.3 73.2 - - - +
314B GLY* 1.3 58.8 + - - +
405B ATP 5.5 3.4 - - - -
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.3 22.2 - - - -
104B VAL 3.3 9.2 - - - -
106B THR* 3.6 7.9 - - - -
249B GLY* 3.3 2.6 - - - -
250B GLY 2.9 23.1 + - - +
291B TYR* 3.2 14.3 + - - +
313B PHE* 1.3 75.6 - - - +
315B ILE* 1.3 64.4 + - - -
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 4.0 1.6 - - - -
104B VAL* 3.1 27.4 + - + +
106B THR* 3.7 22.9 - - + -
235B PHE* 3.3 29.8 - - + -
242B PHE* 3.9 13.5 - - + -
245B VAL* 3.8 28.5 - - + +
246B ALA 4.4 2.7 - - - +
250B GLY 2.8 18.6 - - - +
251B ILE 4.7 0.2 - - - -
252B MET* 4.1 13.5 - - + +
314B GLY* 1.3 73.4 - - - -
316B ARG* 1.3 60.2 + - - +
317B PHE* 3.5 38.5 - - + -
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B SER* 4.7 7.7 + - - +
102B PHE 3.7 12.8 - - - +
103B PHE* 4.1 20.6 - - + -
250B GLY 2.9 7.2 + - - +
251B ILE* 3.1 25.8 - - + +
252B MET 2.9 24.7 + - - +
291B TYR* 3.2 49.9 + - + +
314B GLY 4.1 0.6 - - - -
315B ILE* 1.3 73.9 - - - +
317B PHE* 1.3 62.1 + - - +
318B ASP* 3.1 41.8 + - - -
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Residues in contact with PHE 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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101B SER* 3.1 21.0 - - - -
102B PHE* 3.1 63.5 + + + +
104B VAL* 3.6 18.6 - - + -
231B LEU* 5.5 9.9 - - + -
234B ILE* 5.1 17.0 - - + -
235B PHE* 4.9 11.0 - + - -
252B MET* 2.8 29.6 - - + +
253B GLY 5.1 0.2 - - - +
254B ILE* 5.1 11.0 - - + -
315B ILE* 3.5 41.7 - - + -
316B ARG* 1.3 71.9 - - - +
318B ASP* 1.3 62.5 + - - +
319B ILE* 3.9 0.8 + - + -
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Residues in contact with ASP 318 (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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101B SER* 3.6 12.5 + - - -
251B ILE* 5.0 5.0 - - - +
252B MET 2.9 13.6 + - - +
253B GLY* 3.4 4.9 - - - -
254B ILE 2.9 28.4 + - - +
278B LEU* 5.3 7.0 - - + +
316B ARG* 3.1 45.1 + - - -
317B PHE* 1.3 71.7 - - - +
319B ILE* 1.3 61.7 + - - +
320B LEU* 3.7 16.5 + - + +
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Residues in contact with ILE 319 (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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61B VAL* 4.0 26.5 - - + -
63B THR* 3.7 29.8 - - + -
99B GLY 5.0 1.2 - - - +
100B ASN* 3.3 33.6 + - - +
102B PHE* 3.9 17.7 - - + -
192B ILE* 3.8 29.6 - - + -
194B ASN* 6.4 0.4 - - + -
254B ILE* 3.6 17.7 - - + +
256B ILE* 5.0 8.1 - - + -
317B PHE 3.9 1.7 + - - +
318B ASP* 1.3 72.7 - - - +
320B LEU* 1.3 70.6 + - - +
321B VAL* 4.3 11.9 + - + +
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Residues in contact with LEU 320 (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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254B ILE 2.9 12.4 + - - +
255B GLU* 4.7 8.5 - - + -
256B ILE* 2.9 30.5 + - - +
318B ASP* 4.5 15.9 - - + +
319B ILE* 1.3 83.8 - - - +
321B VAL* 1.3 64.0 + - - +
322B PHE* 4.0 3.1 - - + +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 5.7 8.7 - - + +
59B SER* 4.0 20.0 - - - +
61B VAL* 5.0 2.2 - - + -
194B ASN* 3.6 30.7 - - - +
196B ILE* 4.3 14.1 - - + -
256B ILE* 3.8 24.2 - - + -
258B TRP* 5.7 6.1 - - + -
319B ILE* 4.3 11.4 + - + +
320B LEU* 1.3 77.4 - - - +
322B PHE* 1.3 63.6 + - - +
323B GLY 4.3 1.0 + - - +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE 2.9 14.9 + - - +
257B TYR* 3.2 4.4 - - + +
258B TRP* 2.9 22.6 + - - -
320B LEU* 4.0 3.1 - - + -
321B VAL* 1.3 75.0 - - - +
323B GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 323 (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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56B PRO 5.8 2.3 - - - -
57B LEU* 5.4 16.3 - - - +
258B TRP* 3.1 23.3 - - - -
321B VAL* 4.2 2.0 + - - +
322B PHE* 1.3 75.0 - - - +
324B THR* 1.3 61.2 + - - -
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TRP* 2.9 9.0 + - - +
259B ASP* 5.5 3.6 - - - -
260B CYS* 3.0 36.7 + - - +
323B GLY* 1.3 75.4 - - - -
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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