Contacts of the helix formed by residues 40 - 55 (chain B) in PDB entry 2P7C
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 SER 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B SER* 5.7 1.1 - - - -
38B THR 3.6 2.5 + - - -
39B TRP* 1.3 71.6 - - - +
41B PRO* 1.3 75.5 - - - +
42B LYS* 3.1 17.7 + - - +
43B THR* 2.9 20.0 + - - -
44B ILE* 2.9 23.8 + - - +
16C T 5.4 0.3 - - - +
17C A 5.3 2.4 + - - -
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Residues in contact with PRO 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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30B ILE* 4.1 30.0 - - + +
34B SER* 5.8 4.0 - - - -
40B SER* 1.3 88.7 - - - +
42B LYS* 1.3 69.7 - - + +
44B ILE* 3.8 11.3 - - + +
45B GLN* 3.4 23.9 + - - +
18C A 5.8 0.7 + - - -
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Residues in contact with LYS 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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40B SER* 3.1 13.0 - - - +
41B PRO* 1.3 86.4 - - + +
43B THR* 1.3 64.9 + - - +
45B GLN* 3.2 12.8 + - - +
16C T 3.2 34.6 - - + +
17C A 3.2 65.7 + - + +
18C A 5.2 8.0 + - - +
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Residues in contact with THR 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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39B TRP* 3.5 33.6 - - + -
40B SER* 2.9 29.9 + - - -
42B LYS* 1.3 75.7 - - - +
44B ILE* 1.3 59.6 + - - +
47B MET* 3.2 16.5 - - - +
15C G 3.5 16.8 - - + +
16C T 2.7 57.6 + - - +
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Residues in contact with ILE 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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29B VAL* 4.4 0.4 - - + -
30B ILE* 3.5 38.1 - - + +
33B LEU* 3.6 42.9 - - + +
34B SER* 3.9 11.7 - - - +
39B TRP* 3.4 31.9 - - + +
40B SER 2.9 18.7 + - - +
41B PRO 3.8 4.0 - - - +
42B LYS 3.2 0.2 - - - -
43B THR* 1.3 75.6 - - - +
45B GLN* 1.3 65.8 + - - +
47B MET* 3.3 28.9 + - + +
48B LEU* 3.8 17.4 + - + +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A T 3.1 28.2 + - - +
8A T 2.9 27.3 + - - +
26B THR* 3.3 14.9 - - - +
30B ILE* 3.9 11.3 - - + +
41B PRO 3.4 15.9 - - - +
42B LYS 3.2 5.8 + - - +
44B ILE* 1.3 75.2 - - + +
46B THR* 1.3 60.4 + - - +
48B LEU* 3.1 14.6 + - - +
49B LEU* 2.8 31.6 + - - +
68B TYR* 3.1 27.2 + - - -
16C T 4.0 0.9 - - - -
17C A 3.4 24.9 - - - +
18C A 5.0 1.3 - - - +
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Residues in contact with THR 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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9A A 4.7 0.9 - - - +
43B THR 3.5 7.0 - - - +
45B GLN* 1.3 73.9 - - - +
47B MET* 1.3 76.8 + - - +
49B LEU* 4.5 4.5 - - - +
50B ARG* 3.0 30.3 + - - +
14C T 3.1 29.4 - - + +
15C G 2.7 54.1 + - + +
16C T 3.1 25.4 + - + +
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Residues in contact with MET 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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10B ALA* 4.3 13.7 - - + +
11B GLU* 5.5 0.2 - - - -
14B VAL* 3.9 24.6 - - + +
39B TRP* 3.3 46.0 - - + -
43B THR 3.2 23.1 - - - +
44B ILE* 3.3 20.3 + - + +
46B THR* 1.3 87.1 - - + +
48B LEU* 1.3 59.0 + - + +
51B LEU* 2.9 35.1 - - + +
14C T 3.7 25.1 - - + +
15C G 3.2 23.1 - - - +
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Residues in contact with LEU 48 (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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14B VAL* 5.1 6.7 - - + -
18B ILE* 3.9 28.0 - - + -
29B VAL* 3.6 25.6 - - + -
33B LEU* 4.8 3.4 - - + -
44B ILE* 3.8 18.6 - - + +
45B GLN* 3.1 28.6 + - - +
46B THR 3.0 0.4 - - - -
47B MET* 1.3 80.0 - - + +
49B LEU* 1.3 58.7 + - - +
50B ARG 3.5 0.2 - - - -
51B LEU* 3.4 4.3 - - - +
52B ILE* 3.0 37.3 + - - +
57B LEU* 4.0 11.2 - - + -
68B TYR* 3.5 33.4 - - + +
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Residues in contact with LEU 49 (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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8A T 3.6 51.8 - - + +
9A A 3.5 35.4 - - + +
10A C 4.4 0.4 - - - +
45B GLN 2.8 20.3 + - - +
46B THR* 4.3 1.1 - - - +
48B LEU* 1.3 73.5 - - - +
50B ARG* 1.3 80.3 + - + +
52B ILE* 3.2 9.3 + - + +
53B LYS* 2.8 39.1 + - + +
59B HIS* 5.3 9.2 - - + +
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Residues in contact with ARG 50 (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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10A C 3.3 32.1 - - - +
11A A 3.3 24.6 + - - +
12A T 5.1 0.8 + - - -
46B THR* 3.0 18.3 + - - +
49B LEU* 1.3 78.7 - - + +
51B LEU* 1.3 57.2 + - - +
53B LYS* 3.1 39.3 + - - +
54B LYS* 2.8 65.6 + - - +
13C A 4.1 9.7 - - + +
14C T 2.9 43.5 - - + +
15C G 4.5 2.5 - - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.3 34.8 - - + +
14B VAL* 4.8 8.3 - - + -
15B MET* 5.1 0.7 - - + -
46B THR 4.7 0.7 - - - +
47B MET* 2.9 29.2 - - - +
48B LEU* 3.4 4.5 - - - +
50B ARG* 1.3 73.5 - - - +
52B ILE* 1.3 50.8 + - - +
54B LYS* 3.1 2.8 + - - +
55B GLY 2.7 32.6 + - - -
56B ALA* 2.7 34.4 + - + -
57B LEU* 4.0 21.5 - - + +
13C A 3.8 20.9 - - + +
14C T 3.4 22.4 - - - +
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Residues in contact with ILE 52 (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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8A T 5.8 0.2 - - + -
48B LEU* 3.0 25.5 + - - +
49B LEU* 3.5 8.1 - - + +
51B LEU* 1.3 75.0 - - - +
53B LYS* 1.3 61.6 + - - +
55B GLY* 3.3 11.1 + - - -
57B LEU* 3.3 37.5 - - + +
58B ASN* 3.9 5.2 - - - +
59B HIS* 3.6 48.9 - - + +
68B TYR* 3.5 38.6 - - + -
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Residues in contact with LYS 53 (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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49B LEU* 2.8 26.7 + - + +
50B ARG* 3.4 56.3 - - - +
52B ILE* 1.3 73.9 - - - +
54B LYS* 1.3 65.6 + - + +
55B GLY 3.9 0.2 + - - -
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Residues in contact with LYS 54 (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 ILE* 4.6 9.4 - - - +
5B PRO* 5.9 1.6 - - - +
50B ARG* 2.8 45.6 + - - +
51B LEU 3.4 2.0 - - - +
53B LYS* 1.3 82.6 - - + +
55B GLY* 1.3 57.3 + - - +
56B ALA 3.7 0.7 - - - -
13C A 3.1 67.6 + - + +
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Residues in contact with GLY 55 (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 ILE* 4.4 15.1 - - - +
51B LEU 2.7 10.0 + - - -
52B ILE 3.3 11.1 + - - -
53B LYS 3.5 0.2 - - - -
54B LYS* 1.3 74.3 - - - +
56B ALA* 1.3 61.7 + - - +
57B LEU 3.4 5.8 - - - -
71B ASN* 3.0 25.4 - - - +
72B ILE* 5.1 1.4 - - - +
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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
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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