Contacts of the strand formed by residues 51 - 68 (chain B) in PDB entry 6Q3W
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 LEU 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLY* 3.6 4.7 - - - -
45B THR* 2.9 17.6 + - - +
50B GLY* 1.3 75.5 - - - +
52B VAL* 1.3 62.2 + - - +
200B LEU* 4.6 14.8 - - + -
201B ILE 3.4 3.6 - - - +
202B ASP* 3.7 39.7 - - + +
256B ARG* 4.0 12.8 - - - +
285B ILE* 3.8 33.3 - - + +
288B THR* 3.6 24.6 + - + +
289B ALA* 3.8 23.3 - - + +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE 3.8 4.7 - - - -
42B GLY 3.4 9.6 - - - +
45B THR* 3.3 21.1 - - - +
46B ASP* 3.6 27.4 - - + +
51B LEU* 1.3 72.5 - - - +
53B LEU* 1.3 60.9 + - - +
54B PRO* 3.6 10.5 - - + -
185B MET* 3.8 24.5 - - + -
199B LEU 3.5 0.9 - - - +
200B LEU* 3.6 5.2 - - - +
201B ILE* 3.0 58.1 + - + +
203B CYS* 4.1 7.0 - - - -
288B THR* 4.1 2.7 - - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN* 3.1 3.8 + - - -
40B LEU* 2.9 31.3 + - + +
41B ILE* 2.9 28.2 + - + +
52B VAL* 1.3 74.6 - - - +
54B PRO* 1.3 62.8 - - - +
198B ALA* 4.0 15.5 - - + -
199B LEU 3.6 22.9 - - - +
200B LEU* 3.7 15.0 - - + +
211B VAL* 4.8 6.5 - - + -
288B THR* 4.1 6.3 - - + +
291B ALA* 4.6 0.2 - - + -
292B ALA* 4.1 23.8 - - + +
295B LEU* 4.2 7.9 - - + -
303B PHE* 3.9 31.9 - - + -
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Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 4.0 6.7 - - - -
38B VAL 3.3 12.3 - - - +
39B ASN* 3.2 9.1 - - - +
52B VAL* 3.4 14.6 - - + +
53B LEU* 1.3 91.6 - - - +
55B MET* 1.3 61.6 + - - +
185B MET* 3.9 20.6 - - + -
189B ILE* 3.7 31.0 - - + +
198B ALA* 3.7 2.1 - - - +
199B LEU 2.9 41.2 + - - +
201B ILE* 4.0 7.4 - - + -
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Residues in contact with MET 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.6 1.7 - - - -
38B VAL* 2.7 42.6 + - + +
40B LEU* 4.4 9.6 - - + -
54B PRO* 1.3 76.4 - - - +
56B ALA* 1.3 66.6 + - - +
57B LEU* 4.2 13.2 - - + -
189B ILE* 3.8 7.9 - - - -
197B HIS 4.4 2.9 - - - +
198B ALA* 4.3 17.5 - - + +
213B LEU* 3.6 25.8 - - - -
220B VAL* 4.0 28.3 - - + -
381B SER* 3.4 26.7 - - - +
382B GLN 3.7 13.5 - - - +
383B ALA* 3.7 10.8 - - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO* 3.6 25.8 - - + -
36B GLY 3.7 5.4 - - - -
55B MET* 1.3 84.6 - - - +
57B LEU* 1.3 60.9 + - - +
189B ILE* 3.7 12.9 - - + +
193B GLY* 4.2 13.4 - - - -
197B HIS 5.0 3.2 + - - -
382B GLN 3.5 2.9 - - - +
384B ALA 2.9 43.6 + - - +
385B ASP 3.7 2.9 - - - +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO* 3.4 9.7 - - - +
36B GLY 3.0 14.9 + - - +
37B ARG 3.7 26.2 - - - +
38B VAL* 3.9 31.6 - - + +
55B MET* 4.2 3.1 - - + -
56B ALA* 1.3 77.9 - - - +
58B GLU* 1.3 64.2 + - - +
59B LEU* 3.1 29.0 - - + +
60B MET* 5.2 2.1 - - - +
133B VAL* 6.2 0.2 - - + -
139B LEU* 4.0 27.6 - - + -
222B ILE* 4.0 10.8 - - + -
379B TYR* 6.3 0.4 - - + -
381B SER* 3.4 27.1 - - - +
384B ALA* 3.2 13.8 - - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 4.5 21.8 - - + +
9B VAL* 5.1 8.0 - - + +
57B LEU* 1.3 72.5 - - - +
59B LEU* 1.3 66.7 + - + +
60B MET* 3.6 21.3 + - - +
132B SER* 4.4 1.4 + - - -
380B LEU 4.0 4.7 - - - +
381B SER* 3.2 17.3 + - - +
382B GLN* 2.8 42.5 + - + +
384B ALA* 4.1 13.2 - - + -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 3.5 30.7 - - + -
35B PRO* 3.5 0.2 - - - +
36B GLY 3.0 20.0 + - - +
57B LEU* 3.2 25.3 - - + +
58B GLU* 1.3 77.3 - - - +
60B MET* 1.3 59.6 + - - +
132B SER* 3.4 21.3 - - - +
133B VAL* 3.7 11.9 - - + -
134B PRO* 3.8 21.1 - - + -
139B LEU* 3.9 16.2 - - + -
379B TYR* 3.7 43.5 - - + -
381B SER* 5.8 1.8 - - - +
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Residues in contact with MET 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.8 28.7 - - + -
12B LEU* 3.6 17.6 - - + +
33B SER* 3.7 26.5 - - - +
34B ALA 3.7 14.4 - - - +
35B PRO* 4.1 6.7 - - + -
57B LEU 5.3 1.8 - - - +
58B GLU* 3.7 20.9 - - - +
59B LEU* 1.3 76.3 - - - +
61B THR* 1.3 60.9 + - - +
62B VAL* 3.9 11.2 - - + -
131B SER* 3.2 2.1 - - - -
132B SER* 2.8 33.9 + - - +
133B VAL* 3.6 9.4 - - - +
384B ALA* 6.3 1.3 - - + -
388B LYS* 5.1 12.6 - - - +
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Residues in contact with THR 61 (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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33B SER* 3.2 4.3 - - - -
34B ALA 3.1 29.9 + - - -
60B MET* 1.3 72.2 - - - +
62B VAL* 1.3 64.5 + - - +
63B LEU* 4.1 13.0 - - + -
129B VAL* 4.1 5.4 - - + -
130B VAL 3.3 12.6 - - - +
131B SER* 2.8 19.6 + - - -
133B VAL* 4.3 0.4 - - - +
141B SER 4.1 1.2 + - - -
144B SER* 2.7 34.4 + - - -
145B LEU* 4.0 31.4 + - + +
148B ALA* 3.9 4.1 - - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.8 24.9 - - + -
13B LEU* 4.1 19.7 - - + +
16B ALA* 4.4 2.0 - - + -
31B ALA* 5.3 0.4 - - + -
32B VAL 3.3 10.8 - - - +
33B SER* 3.9 5.8 - - - -
60B MET* 3.9 18.4 - - - -
61B THR* 1.3 77.7 - - - +
63B LEU* 1.3 65.4 + - - +
64B VAL* 4.0 24.7 - - + -
128B VAL 3.6 1.6 - - - +
129B VAL* 3.6 3.6 - - - -
130B VAL* 2.7 50.1 + - + +
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Residues in contact with LEU 63 (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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30B LEU 4.0 0.2 - - - +
31B ALA* 3.5 2.4 - - - -
32B VAL* 2.8 53.3 + - + +
61B THR* 4.1 10.5 + - + -
62B VAL* 1.3 75.9 - - - +
64B VAL* 1.3 63.7 + - - +
65B GLY 4.2 0.6 + - - -
75B LEU* 6.0 0.9 - - + -
110B VAL* 5.6 2.9 - - + -
125B PHE* 5.4 4.3 - - + -
127B ALA* 4.6 12.3 - - + -
128B VAL 3.6 2.0 - - - +
129B VAL* 3.7 32.3 - - + -
145B LEU* 4.2 7.6 - - + -
148B ALA* 3.9 19.7 - - + +
149B THR* 4.0 29.6 - - + +
152B PHE* 4.2 21.5 - - + -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.6 30.7 - - + -
16B ALA* 4.0 32.8 - - + +
17B ARG* 4.2 5.2 - - + -
20B PHE* 3.2 7.1 - - + -
28B PRO* 3.5 31.2 - - + -
30B LEU 3.3 9.4 - - - +
31B ALA* 3.8 7.0 - - + -
62B VAL* 4.0 5.6 - - + -
63B LEU* 1.3 78.3 - - - +
65B GLY* 1.3 57.8 + - - +
127B ALA* 4.2 1.8 - - - -
128B VAL* 2.8 35.2 + - + +
152B PHE* 4.7 0.2 - - - -
392B LEU* 4.4 0.7 - - + -
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Residues in contact with GLY 65 (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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20B PHE* 3.4 9.4 - - - -
28B PRO* 3.9 1.1 - - - +
29B GLU 3.1 1.2 + - - -
30B LEU* 2.8 40.8 + - - +
64B VAL* 1.3 75.6 - - - +
66B SER* 1.3 65.2 + - - -
126B SER 3.1 14.4 - - - -
127B ALA* 4.0 0.2 - - - -
152B PHE* 3.8 16.7 - - - -
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Residues in contact with SER 66 (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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20B PHE* 4.0 10.3 - - - -
27B GLU 3.9 3.1 + - - -
28B PRO* 3.4 7.4 - - - +
29B GLU* 2.7 37.9 + - - +
65B GLY* 1.3 69.7 + - - -
67B PRO* 1.3 77.5 - - - +
125B PHE* 3.2 7.9 - - - +
126B SER* 2.9 31.9 + - - -
152B PHE* 3.8 5.6 - - - -
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 3.9 28.6 - - + +
30B LEU* 4.9 7.4 - - + -
66B SER* 1.3 97.6 - - - +
68B ARG* 1.3 61.4 + - - +
123B PRO* 5.1 6.1 - - + -
124B GLY 3.5 6.7 - - - +
126B SER* 5.0 0.5 + - - -
156B LEU* 3.7 27.1 - - + -
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Residues in contact with ARG 68 (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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67B PRO* 1.3 78.2 - - - +
71B GLY 4.9 6.9 + - - -
72B LEU* 4.5 8.7 - - + +
123B PRO* 3.8 9.1 - - - +
124B GLY* 2.8 44.2 + - - +
125B PHE* 3.8 7.4 - - - +
126B SER* 4.9 1.1 - - - +
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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