Contacts of the strand formed by residues 34 - 47 (chain B) in PDB entry 3Q2P
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 PHE 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLN* 3.6 37.2 - - + -
16B ALA* 3.7 25.8 - - + -
17B LYS* 3.7 41.7 - - + -
20B VAL* 4.0 16.1 - - + +
21B ASP* 5.9 0.7 - - - +
32B LEU 4.0 2.0 + - - -
33B THR* 1.3 78.2 - - - +
35B ASN* 1.3 74.8 + - - +
36B LYS* 3.7 11.4 - - - -
64B VAL* 3.9 17.0 - - + -
66B ALA* 4.2 7.9 - - - -
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Residues in contact with ASN 35 (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 THR* 3.4 16.9 + - - +
34B PHE* 1.3 90.2 + - - +
36B LYS* 1.3 65.1 + - + +
65B TYR* 2.8 24.9 + - + +
66B ALA* 3.3 5.9 + - - -
67B SER* 3.0 7.8 + - - +
68B ASP* 2.7 42.0 + - - -
88C ARG* 5.6 3.8 - - - +
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Residues in contact with LYS 36 (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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8B ILE* 4.3 14.1 - - - +
13B GLN* 3.6 14.0 - - - +
34B PHE* 3.7 14.4 - - - -
35B ASN* 1.3 86.8 - - + +
37B ALA* 1.3 75.3 + - - +
38B ILE* 3.6 23.6 + - + +
64B VAL* 3.4 1.4 - - - -
65B TYR* 2.7 41.4 + - + +
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Residues in contact with ALA 37 (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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8B ILE* 4.3 3.5 - - + +
12B THR* 4.3 20.6 - - + +
13B GLN* 2.8 38.9 + - - +
16B ALA* 3.7 22.0 - - + -
34B PHE* 4.2 1.8 - - - -
36B LYS* 1.3 86.7 + - - +
38B ILE* 1.3 63.1 + - - +
41B CYS* 4.9 1.3 - - - -
62B LEU* 5.4 0.4 - - + -
63B TYR 3.4 10.8 - - - +
64B VAL* 4.2 1.6 - - - +
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Residues in contact with ILE 38 (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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8B ILE* 3.6 11.2 - - + -
36B LYS* 3.6 24.9 + - - +
37B ALA* 1.3 79.5 - - - +
39B ARG* 1.3 73.2 + - - +
41B CYS* 3.2 19.9 - - - -
63B TYR* 3.2 23.9 + - + +
65B TYR* 4.0 35.9 - - + +
70B LEU* 4.2 18.8 - - + -
95B PRO* 5.6 1.6 - - + -
96B PRO* 4.4 9.0 - - + -
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Residues in contact with ARG 39 (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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3A TRP* 5.1 8.1 + - + +
5B ILE* 4.1 16.6 - - - +
6B ILE 4.1 12.1 + - - +
7B ASP* 3.5 31.7 - - - +
8B ILE* 3.6 29.5 - - + +
38B ILE* 1.3 87.1 - - - +
40B PRO* 1.3 70.8 - - + +
41B CYS 5.1 0.2 - - - +
63B TYR* 4.2 1.0 - - - -
96B PRO* 3.6 13.7 - - - +
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Residues in contact with PRO 40 (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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3A TRP* 3.7 41.1 - - + +
42A MET* 3.8 32.3 - - + -
5B ILE* 4.7 9.2 - - + -
39B ARG* 1.3 88.2 - - + +
41B CYS* 1.3 65.3 + - - +
42B MET* 4.3 2.0 + - - +
61B GLN 4.3 2.9 - - - +
63B TYR* 3.5 23.9 - - + -
72B ARG* 5.2 2.6 + - - -
96B PRO* 3.5 21.8 - - + -
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Residues in contact with CYS 41 (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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5B ILE* 3.6 7.9 - - - +
6B ILE* 3.0 45.2 + - + +
7B ASP 4.6 1.3 - - - +
8B ILE* 4.4 4.0 - - + +
12B THR* 3.9 22.4 - - + -
37B ALA* 4.9 0.4 - - - -
38B ILE 3.2 30.1 - - - -
39B ARG* 4.1 1.8 - - - +
40B PRO* 1.3 76.5 - - - +
42B MET* 1.3 62.4 + - - +
61B GLN 3.6 4.7 - - - +
62B LEU* 3.7 35.4 - - + -
63B TYR 3.9 3.4 - - - -
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Residues in contact with MET 42 (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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5A ILE* 4.3 8.5 - - + -
40A PRO* 4.2 23.3 - - + -
42A MET* 3.7 38.8 - - + +
61A GLN* 5.3 0.7 - - - +
63A TYR* 5.9 1.8 - - + -
3B TRP* 4.0 14.4 - - + -
4B GLU 3.5 5.4 - - - +
5B ILE* 4.3 9.0 - - + -
6B ILE* 5.0 1.6 - - - -
40B PRO 5.5 1.6 - - - +
41B CYS* 1.3 77.8 - - - +
43B LYS* 1.3 60.5 + - - +
59B GLU 3.7 0.5 - - - +
60B TYR* 3.2 10.0 - - - +
61B GLN* 3.0 56.1 + - + +
62B LEU* 4.9 0.3 - - - +
72B ARG* 3.2 31.0 - - - +
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Residues in contact with LYS 43 (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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2B GLU 3.6 1.4 - - - +
3B TRP* 3.3 6.2 - - - -
4B GLU* 2.9 59.0 + - + +
6B ILE* 3.8 25.5 - - + +
42B MET* 1.3 74.9 - - - +
44B LYS* 1.3 66.6 + - - +
45B THR* 3.7 5.8 - - - -
58B TYR* 3.6 33.2 + - - -
59B GLU 3.4 2.7 - - - -
60B TYR* 3.5 33.9 + - + -
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Residues in contact with LYS 44 (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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96A PRO 3.1 28.7 + - - -
1B GLY* 4.2 14.8 - - - -
2B GLU 3.3 8.3 - - - +
3B TRP* 3.4 43.7 - - + +
43B LYS* 1.3 74.5 - - - +
45B THR* 1.3 74.0 + - - +
46B ILE* 3.8 20.0 - - + +
58B TYR* 3.2 10.2 - - - +
59B GLU* 2.6 59.3 + - + +
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Residues in contact with THR 45 (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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0B MET 3.5 1.4 - - - +
1B GLY* 3.4 5.7 - - - -
2B GLU* 2.9 32.2 + - - -
4B GLU* 4.4 5.5 + - - -
43B LYS* 3.7 12.2 + - - +
44B LYS* 1.3 74.4 - - - +
46B ILE* 1.3 63.4 + - - +
47B TYR* 3.3 42.1 + - + +
55B ILE* 4.1 15.0 - - + -
57B GLY 3.9 2.2 - - - -
58B TYR* 3.7 26.7 - - + -
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Residues in contact with ILE 46 (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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0B MET 3.4 10.3 - - - +
1B GLY* 5.3 0.7 - - - -
44B LYS* 3.8 22.4 - - + +
45B THR* 1.3 75.2 - - - +
47B TYR* 1.3 65.1 + - - +
55B ILE* 3.7 2.9 - - - +
56B LYS* 2.7 50.3 + - + +
57B GLY* 3.0 29.2 + - - +
58B TYR 4.3 0.9 - - - +
59B GLU* 3.7 32.8 - - + +
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Residues in contact with TYR 47 (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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0B MET* 2.8 52.1 + - + +
2B GLU* 3.6 26.3 + - + +
45B THR* 3.3 40.6 + - + +
46B ILE* 1.3 80.4 - - - +
48B GLU* 1.3 65.1 + - - +
49B ASN 3.8 19.1 - - - +
53B ARG* 3.2 54.5 + - + -
54B GLU 3.2 7.2 - - - +
55B ILE* 3.9 19.3 - - + -
56B LYS* 4.6 1.6 - - - +
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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