Contacts of the helix formed by residues 29 - 42 (chain B) in PDB entry 2X2D
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 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B PHE* 2.9 28.0 + - + +
28B LYS* 1.3 77.7 - - + +
30B PRO* 1.4 61.8 - - - +
32B THR* 4.3 4.3 - - - -
33B ALA* 3.0 26.7 + - - +
86B GLU* 3.2 17.7 - - + +
87B ASN* 3.5 29.8 - - - +
90B LEU* 4.9 2.9 - - + -
127B VAL* 4.1 12.1 - - + -
128B VAL 3.8 12.1 - - - +
129B PHE* 3.5 35.7 - - + +
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Residues in contact with PRO 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.4 25.5 - - + +
27B ASP 5.2 1.3 - - - +
28B LYS 3.6 7.4 - - - +
29B VAL* 1.4 85.4 - - - +
31B LYS* 1.3 53.8 + - + +
33B ALA* 3.8 1.4 - - - +
34B GLU* 3.0 31.3 + - - +
86B GLU* 2.8 18.8 - - + +
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Residues in contact with LYS 31 (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 PRO* 1.3 74.7 - - - +
32B THR* 1.3 65.3 + - - +
34B GLU* 4.6 0.7 - - - -
35B ASN* 3.1 11.8 + - - +
79B TYR* 2.6 71.6 + - + +
83B PHE* 4.3 11.5 - - + +
84B GLU* 2.4 39.7 + - + +
86B GLU* 2.9 20.2 + - + +
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.9 5.2 - - - -
31B LYS* 1.3 73.4 - - - +
33B ALA* 1.3 67.7 + - - +
35B ASN* 3.4 5.0 + - - +
36B PHE* 3.2 21.5 + - - +
83B PHE* 3.7 22.3 - - + -
86B GLU* 2.7 26.8 + - - +
100B MET* 3.6 35.5 - - + +
108B ASN* 5.9 0.2 - - - -
127B VAL* 4.2 9.7 - - + +
129B PHE* 3.6 25.1 - - + -
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Residues in contact with ALA 33 (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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4B PRO* 5.4 2.0 - - + -
24B LEU* 3.7 20.1 - - + +
25B PHE 4.1 3.4 - - - +
26B ALA* 3.6 33.4 - - + +
29B VAL* 3.0 19.6 + - + +
30B PRO 3.8 1.8 - - - +
32B THR* 1.3 77.5 - - - +
34B GLU* 1.3 56.0 + - - +
36B PHE* 3.3 1.7 + - - +
37B ARG* 2.9 29.7 + - - +
129B PHE* 4.3 12.4 - - - +
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Residues in contact with GLU 34 (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 PRO 3.0 19.8 + - - +
31B LYS* 4.6 0.2 - - - -
32B THR 3.3 0.2 - - - -
33B ALA* 1.3 73.7 - - - +
35B ASN* 1.3 66.9 + - - +
37B ARG* 2.6 47.1 + - - -
38B ALA* 2.9 30.0 + - - +
43B GLU* 4.5 0.7 - - - +
44B LYS* 5.2 4.2 + - - -
78B ILE* 3.9 14.1 - - + +
79B TYR* 3.8 10.1 - - + +
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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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31B LYS 3.1 12.2 + - - +
32B THR 3.5 8.9 + - - +
34B GLU* 1.3 80.0 - - - +
36B PHE* 1.3 59.0 + - - +
38B ALA* 3.9 1.2 - - - +
39B LEU* 3.0 46.9 + - - +
48B TYR* 4.9 1.0 + - - -
77B SER* 3.2 5.2 - - - -
78B ILE* 2.8 41.6 + - - +
79B TYR* 3.8 5.9 + - + -
83B PHE* 3.5 22.5 - - + -
100B MET* 4.2 7.7 - - - +
109B GLY 2.8 25.7 + - - -
110B SER* 4.4 0.8 - - - +
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Residues in contact with PHE 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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6B VAL* 3.8 15.5 - - + -
8B PHE* 3.5 22.7 - + - -
22B PHE* 4.3 6.1 - + - -
24B LEU* 3.7 22.4 - - + -
32B THR 3.2 5.4 + - - +
33B ALA 3.9 4.9 - - - +
35B ASN* 1.3 78.1 - - - +
37B ARG* 1.3 63.1 + - - +
39B LEU* 3.4 2.3 + - - +
40B SER* 2.9 38.6 + - - -
48B TYR* 3.5 32.0 - + - +
98B LEU* 3.9 20.9 - - + -
100B MET* 5.8 2.0 - - - -
112B PHE* 3.8 26.9 - + + -
129B PHE* 3.4 34.1 - + + -
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Residues in contact with ARG 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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4B PRO* 4.1 16.8 - - + -
6B VAL* 4.2 14.0 - - + +
24B LEU* 3.8 12.9 - - + +
33B ALA 2.9 17.9 + - - +
34B GLU* 2.6 46.0 + - - +
36B PHE* 1.3 78.0 - - - +
38B ALA* 1.3 65.6 + - - +
40B SER* 3.1 4.3 + - - -
41B THR* 3.0 31.9 + - - +
43B GLU* 2.8 43.5 + - - -
163B GLN* 2.8 50.6 + - + +
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Residues in contact with ALA 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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34B GLU* 2.9 31.2 + - - +
37B ARG* 1.3 84.9 - - - +
39B LEU* 1.3 57.5 + - - +
41B THR* 3.0 9.9 + - - -
42B GLY* 3.0 24.3 + - - -
43B GLU* 3.6 8.8 + - + +
44B LYS* 4.2 14.1 + - - -
46B PHE 4.8 0.5 - - - +
78B ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 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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35B ASN* 3.0 47.2 + - - +
36B PHE 3.8 0.2 - - - +
38B ALA* 1.3 77.5 - - - +
40B SER* 1.3 59.6 + - - +
41B THR 3.7 0.2 + - - -
42B GLY* 3.8 3.7 + - - -
46B PHE* 3.8 38.6 - - + +
47B GLY* 3.4 11.3 - - - -
48B TYR* 3.0 60.0 + - + +
49B LYS 4.7 0.9 + - - -
67B PHE* 3.8 15.5 - - + -
76B LYS 3.9 4.3 - - - +
78B ILE* 4.1 8.3 - - + -
110B SER* 3.7 15.5 - - - -
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Residues in contact with SER 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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6B VAL* 3.2 36.8 - - - +
8B PHE* 3.6 8.4 - - - -
36B PHE* 2.9 22.8 + - - -
37B ARG 3.1 5.5 + - - -
39B LEU* 1.3 78.6 - - - +
41B THR* 1.3 58.8 + - - +
48B TYR* 3.6 15.3 - - - -
161B CYS* 3.2 32.3 - - - +
162B GLY* 3.2 9.8 + - - -
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Residues in contact with THR 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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37B ARG* 3.0 22.2 + - - +
38B ALA 3.0 11.1 + - - -
40B SER* 1.3 76.9 - - - +
42B GLY* 1.3 59.6 + - - +
43B GLU* 2.6 39.0 + - - +
161B CYS 5.0 1.4 - - - +
162B GLY* 4.4 4.7 - - - -
163B GLN* 3.9 28.3 - - + +
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Residues in contact with GLY 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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38B ALA 3.0 5.6 + - - -
39B LEU 3.8 4.6 + - - -
40B SER 3.4 2.8 - - - -
41B THR* 1.3 77.6 - - - +
43B GLU* 1.3 58.2 + - - +
44B LYS 3.1 3.8 - - - -
45B GLY* 3.1 22.3 + - - -
46B PHE 3.8 19.0 + - - -
47B GLY* 5.0 0.9 - - - -
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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