Contacts of the helix formed by residues 41 - 53 (chain B) in PDB entry 4K2S
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 ARG 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A TYR* 3.0 48.7 + - + +
52A HIS* 3.2 43.3 + - + +
53A VAL* 4.6 7.5 - - - +
71A TYR 5.8 0.2 + - - -
72A LEU* 4.5 13.7 + - - +
75A GLY 4.6 3.4 + - - -
76A ALA* 3.7 32.4 - - + +
78A TRP* 4.6 10.8 - - + -
38B LEU* 3.0 30.3 + - + +
39B ASN 3.2 4.2 - - - +
40B GLY* 1.3 95.3 + - - +
42B GLU* 1.3 65.6 + - - +
44B ALA* 3.1 17.3 + - - +
45B VAL* 3.8 2.9 + - - +
179B PRO* 6.3 0.8 - - - +
391B SER* 4.9 10.1 + - - -
392B LEU 6.1 0.2 - - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 3.3 8.5 + - - -
17B ARG* 3.0 25.6 + - - -
18B ASN* 3.7 28.8 + - + +
20B VAL* 4.0 20.3 - - + +
36B ALA 5.7 0.2 - - - -
37B THR* 4.3 7.9 - - + -
38B LEU* 3.4 22.9 - - - +
39B ASN* 3.4 1.6 - - - +
40B GLY* 3.0 28.8 + - - -
41B ARG* 1.3 80.0 + - - +
43B MET* 1.3 64.4 + - - +
44B ALA 3.3 0.5 + - - -
45B VAL* 3.4 6.2 + - - +
46B ALA* 3.2 19.6 + - - +
387B TYR* 4.4 13.8 + - + -
390B ALA 4.5 4.0 - - - +
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Residues in contact with MET 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.5 16.3 - - + +
51A GLU* 3.5 31.9 - - + +
52A HIS* 2.9 12.0 + - - +
12B VAL* 4.5 17.5 - - + -
20B VAL* 5.5 0.2 - - - -
42B GLU* 1.3 76.9 - - - +
44B ALA* 1.3 59.5 + - - +
46B ALA* 3.7 21.5 - - + +
47B ALA* 3.0 23.0 + - - +
387B TYR* 3.9 34.1 - - + -
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Residues in contact with ALA 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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44A ALA* 3.9 14.5 - - - +
47A ALA* 4.2 4.0 - - - +
48A TYR* 3.7 41.3 - - + -
52A HIS* 3.9 3.6 + - + -
83A VAL* 4.7 0.2 - - + -
41B ARG 3.1 12.6 + - - +
43B MET* 1.3 79.5 - - - +
45B VAL* 1.3 57.2 + - - +
47B ALA* 3.5 2.1 + - - +
48B TYR* 2.9 27.9 + - - +
83B VAL* 3.7 16.7 - - + +
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Residues in contact with VAL 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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20B VAL* 5.3 0.4 - - + -
36B ALA* 3.3 36.6 - - + +
38B LEU* 3.8 39.5 - - + -
41B ARG 3.8 1.8 + - - +
42B GLU 3.4 6.1 + - - +
43B MET 3.3 0.2 - - - -
44B ALA* 1.3 74.6 - - - +
46B ALA* 1.3 65.4 + - - +
48B TYR* 3.2 2.5 + - - +
49B LEU* 2.9 28.7 + - + +
83B VAL* 3.9 23.1 - - + +
86B THR* 4.0 11.4 - - + -
87B ALA* 4.1 13.7 - - + +
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Residues in contact with ALA 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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10B THR* 4.9 3.8 - - - +
12B VAL* 4.5 8.3 - - + -
20B VAL* 4.5 19.4 - - + +
42B GLU 3.2 13.2 + - - +
43B MET* 3.7 31.9 - - + +
44B ALA 3.4 0.2 - - - -
45B VAL* 1.3 77.2 - - - +
47B ALA* 1.3 51.8 + - - +
49B LEU* 3.8 3.7 - - - +
50B ASP* 2.7 50.2 + - - +
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Residues in contact with ALA 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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43A MET* 3.4 30.7 - - + +
44A ALA* 4.7 2.0 - - - -
47A ALA* 3.6 9.9 - - + -
43B MET 3.0 18.4 + - - +
44B ALA 3.9 2.2 - - - +
46B ALA* 1.3 75.0 - - - +
48B TYR* 1.3 65.8 + - - +
50B ASP* 4.3 6.3 - - - +
51B GLU* 2.9 29.9 + - + +
52B HIS* 4.0 1.1 - - - -
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Residues in contact with TYR 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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38A LEU* 5.9 0.4 - - + -
41A ARG* 3.0 44.6 + - + +
44A ALA* 3.7 23.4 - - + +
82A PRO* 6.1 0.4 - - + -
83A VAL* 4.1 7.6 - - + -
44B ALA 2.9 17.6 + - - +
45B VAL* 3.4 5.8 - - - +
47B ALA* 1.3 74.4 - - - +
49B LEU* 1.3 61.7 + - - +
52B HIS* 3.2 24.5 + - - +
53B VAL* 3.2 22.7 + - + -
72B LEU 5.0 0.9 + - - -
76B ALA* 3.5 12.8 - - - +
78B TRP 4.9 0.5 + - - -
83B VAL* 3.8 17.7 - - + -
84B THR* 3.5 39.8 + - - +
87B ALA* 3.4 24.9 - - + -
88B ILE* 5.6 3.9 - - + +
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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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10B THR* 3.8 25.6 - - + -
20B VAL* 5.1 0.7 - - + -
22B LEU* 4.4 12.6 - - + -
36B ALA* 3.7 29.6 - - + -
45B VAL* 2.9 22.3 + - + +
46B ALA 3.8 2.7 - - - +
48B TYR* 1.3 75.2 - - - +
50B ASP* 1.3 63.3 + - - +
53B VAL* 3.2 25.4 + - + -
54B VAL* 2.8 33.2 + - + +
87B ALA* 3.6 35.0 - - + +
90B ALA* 4.3 6.5 - - + -
91B VAL* 4.2 6.7 - - + -
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Residues in contact with ASP 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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389A ARG* 5.1 0.5 + - - -
9B TYR* 5.3 0.3 - - - -
10B THR* 2.8 37.5 + - - +
46B ALA* 2.7 32.5 + - - +
47B ALA* 4.1 4.3 - - - +
49B LEU* 1.3 73.9 - - - +
51B GLU* 1.3 62.9 + - + +
54B VAL* 3.9 10.9 - - - +
55B PRO* 3.5 15.1 - - - +
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Residues in contact with GLU 51 (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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43A MET* 3.5 17.7 - - + +
387A TYR* 2.6 42.6 + - - +
389A ARG* 3.1 49.4 + - - +
47B ALA* 2.9 15.9 + - + +
50B ASP* 1.3 79.5 - - + +
52B HIS* 1.3 74.8 + - + +
55B PRO* 3.7 4.0 - - - +
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Residues in contact with HIS 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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40A GLY 3.1 14.5 + - - -
41A ARG* 3.2 48.8 + - + +
42A GLU* 3.4 20.2 - - - -
43A MET 3.0 24.8 + - - -
44A ALA* 4.1 4.5 - - + -
387A TYR* 3.5 13.6 + - - -
389A ARG* 4.9 6.0 - - + +
390A ALA 5.7 2.1 + - - -
391A SER* 5.1 7.8 + - - -
47B ALA 4.0 8.7 - - - -
48B TYR* 3.2 12.5 + - - +
51B GLU* 1.3 108.4 + - + +
53B VAL* 1.3 65.4 + - - +
54B VAL 3.9 0.2 - - - -
55B PRO* 4.0 4.9 - - - +
56B ALA* 4.4 9.9 - - - +
72B LEU* 5.9 0.2 - - - +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 4.7 3.8 - - - +
48B TYR* 3.2 38.3 + - + +
49B LEU* 3.2 21.5 + - + +
52B HIS* 1.3 79.5 - - - +
54B VAL* 1.3 68.7 + - - +
55B PRO 3.3 1.3 - - - -
56B ALA* 2.9 18.3 + - - +
57B LEU* 3.2 17.4 + - + +
72B LEU* 4.0 29.2 - - + -
87B ALA* 4.7 2.2 - - + -
88B ILE* 6.3 0.7 - - + -
91B VAL* 3.9 28.0 - - + -
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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