Contacts of the helix formed by residues 30 - 42 (chain B) in PDB entry 4DUQ
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 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU* 4.9 9.1 + - - +
29B LEU* 1.3 76.7 - - - +
31B LYS* 1.3 65.4 + - - +
32B GLY* 3.4 4.9 + - - -
33B GLU* 2.8 39.8 + - - +
34B MET* 2.8 20.8 + - - +
59B MET* 3.9 1.8 - - - -
69B GLN* 3.4 20.8 + - - -
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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 SER* 1.3 74.6 - - - +
32B GLY* 1.3 58.3 + - - +
34B MET* 3.4 1.9 + - - +
35B LYS* 2.9 28.2 + - - +
52B GLU* 2.6 37.9 + - - -
55B LEU* 3.6 23.6 - - + +
56B LYS* 3.4 25.4 - - + +
59B MET* 3.7 29.3 - - + +
68B GLN 4.6 4.2 + - - +
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Residues in contact with GLY 32 (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 SER* 3.2 5.6 + - - -
31B LYS* 1.3 78.2 - - - +
33B GLU* 1.3 64.7 + - - +
35B LYS* 3.4 10.2 + - - +
36B GLU* 3.1 22.5 + - - +
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Residues in contact with GLU 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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19B TYR* 3.1 28.2 - - - +
20B SER 3.1 3.1 - - - +
22B GLN* 3.7 19.1 - - + +
23B GLU* 2.8 35.0 + - + +
28B LYS 2.9 4.9 - - - +
29B LEU* 3.2 10.4 - - + -
30B SER* 2.8 36.1 + - - +
32B GLY* 1.3 75.1 - - - +
34B MET* 1.3 59.3 + - - +
36B GLU* 3.3 4.3 + - - +
37B LEU* 2.9 28.4 + - - +
103B CA 2.4 30.0 - - - -
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Residues in contact with MET 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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29B LEU* 3.9 29.5 - - + +
30B SER 2.8 16.8 + - - +
31B LYS 3.7 3.8 - - - +
33B GLU* 1.3 75.1 - - - +
35B LYS* 1.3 64.9 + - - +
37B LEU* 3.2 16.7 + - - -
38B LEU* 2.8 52.2 + - + +
55B LEU* 4.2 3.1 - - + -
58B LEU* 4.9 2.9 - - + -
59B MET* 3.8 20.9 - - - -
62B LEU* 4.0 17.9 - - + -
70B VAL* 3.9 24.9 - - + -
75B TYR* 5.2 1.6 - - + -
78B PHE* 4.4 12.1 - - + -
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Residues in contact with LYS 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 2.9 17.2 + - - +
32B GLY* 3.5 11.4 - - - +
34B MET* 1.3 76.8 - - - +
36B GLU* 1.3 63.8 + - - +
38B LEU 3.4 0.2 + - - -
39B HIS* 3.0 19.7 + - + +
50B VAL* 3.1 47.1 + - + +
52B GLU* 4.8 9.8 + - - +
55B LEU* 3.6 24.2 - - + +
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Residues in contact with GLU 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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19B TYR* 3.5 9.9 - - + -
22B GLN* 2.9 38.6 + - - +
32B GLY 3.1 10.3 + - - +
33B GLU 3.6 7.4 - - - +
35B LYS* 1.3 79.6 - - - +
37B LEU* 1.3 61.7 - - - +
39B HIS* 3.6 5.3 - - + +
40B LYS* 2.9 69.1 + - - +
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Residues in contact with LEU 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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5A LEU* 4.3 11.9 - - + -
15B THR* 4.4 9.0 - - + +
16B PHE* 4.8 0.7 - - - -
19B TYR* 3.8 42.3 - - + -
29B LEU* 4.1 17.3 - - + -
33B GLU 2.9 16.3 + - - +
34B MET* 3.6 16.6 - - - +
36B GLU* 1.3 74.6 - - - +
38B LEU* 1.3 60.3 + - - +
41B GLU* 2.7 39.2 + - + +
42B LEU* 3.5 24.4 + - + -
75B TYR* 4.1 25.4 - - + -
78B PHE* 5.0 1.3 - - + -
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Residues in contact with LEU 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 MET* 2.8 29.2 + - + +
35B LYS 3.7 3.1 - - - +
37B LEU* 1.3 77.0 - - + +
39B HIS* 1.3 61.8 + - - +
42B LEU* 2.9 32.7 + - + +
45B PHE* 6.4 0.2 - - + -
46B VAL* 3.1 41.9 - - + +
50B VAL* 4.0 14.1 - - + -
55B LEU* 3.8 22.9 - - + -
58B LEU* 3.7 24.2 - - + -
78B PHE* 3.8 28.9 - - + -
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Residues in contact with HIS 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 LYS* 3.0 18.0 + - + +
36B GLU* 3.2 8.0 + - - +
38B LEU* 1.3 78.2 - - - +
40B LYS* 1.3 76.7 + - + +
43B PRO* 3.8 17.3 - - - +
46B VAL* 4.2 4.0 - - - -
47B GLY 4.4 1.8 - - - +
48B GLU* 2.9 34.0 + - - -
49B LYS* 4.6 0.7 - - - -
50B VAL* 3.8 15.9 - - + +
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Residues in contact with LYS 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 SER* 3.7 12.1 - - - -
19B TYR* 3.5 22.7 - - - +
36B GLU* 2.9 49.2 + - + +
39B HIS* 1.3 94.3 - - + +
41B GLU* 1.3 62.5 + - + +
43B PRO* 3.9 6.4 - - - +
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Residues in contact with GLU 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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3A SER* 2.6 26.5 + - - -
4A SER* 4.0 6.9 + - - -
5A LEU* 3.5 41.0 + - + +
6A GLU* 3.4 8.5 - - - +
15B THR* 3.9 14.3 + - + +
18B LYS* 4.3 11.3 + - - +
19B TYR* 2.8 41.6 + - + +
37B LEU* 2.7 24.3 + - + +
40B LYS* 1.3 76.1 - - - +
42B LEU* 1.3 61.2 + - - +
43B PRO* 3.2 6.1 - - - -
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Residues in contact with LEU 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 LEU* 3.8 20.9 - - + -
6A GLU* 3.4 5.8 - - + -
9A LEU* 3.8 20.2 - - + -
37B LEU* 3.5 12.3 + - + -
38B LEU* 2.9 28.2 + - + +
41B GLU* 1.3 88.1 - - - +
43B PRO* 1.4 59.7 - - - +
44B SER 3.1 2.0 - - - -
45B PHE* 3.0 30.2 + - + -
46B VAL* 2.9 24.8 + - - +
78B PHE* 3.7 24.9 - - + -
79B LEU* 4.4 0.2 - - + -
82B ILE* 3.6 20.2 - - + -
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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