Contacts of the helix formed by residues 62 - 71 (chain B) in PDB entry 5DQZ
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 HIS 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU 3.2 18.5 + - - -
55A GLU 3.3 12.3 - - - -
56A PRO* 3.7 17.2 - - + +
57A GLY 4.2 4.5 - - - +
58A THR* 2.9 32.2 + - - +
60A VAL* 6.2 0.2 - - - +
77A TRP* 3.8 24.6 - + + +
78A VAL 2.8 32.3 + - - -
86A TYR* 3.7 25.6 - + - -
61B SER* 1.3 72.0 - - - +
63B ALA* 1.3 66.9 + - - +
65B VAL* 3.2 4.7 + - - +
66B ARG* 3.0 24.1 + - + +
8H G 5.3 1.7 + - - -
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Residues in contact with ALA 63 (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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27B VAL* 3.5 15.7 - - + +
61B SER* 3.3 3.7 + - - +
62B HIS* 1.3 81.9 + - - +
64B ALA* 1.3 58.3 + - - +
66B ARG* 3.4 11.5 + - - +
67B LEU* 2.9 30.3 + - - +
8H G 4.7 1.0 + - - +
9H T 3.6 32.5 - - - -
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Residues in contact with ALA 64 (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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25B ILE* 3.7 33.0 - - + +
26B ASP 4.4 0.4 - - - +
27B VAL* 3.4 14.5 - - + +
32B PHE* 3.5 13.5 - - + -
60B VAL* 3.7 7.0 - - + -
61B SER* 3.1 23.4 + - - +
63B ALA* 1.3 74.8 - - - +
65B VAL* 1.3 59.9 + - - +
67B LEU* 3.3 1.9 + - - +
68B ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 65 (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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77A TRP* 3.6 40.4 - - + +
87A ALA* 3.6 16.2 - - + -
60B VAL* 3.6 26.7 - - + +
61B SER 3.2 7.2 + - - +
62B HIS 3.2 6.6 + - - +
64B ALA* 1.3 76.0 - - - +
66B ARG* 1.3 64.9 + - - +
68B ALA* 3.3 2.8 + - - +
69B ALA* 3.0 22.2 + - - +
75B LEU* 4.1 14.4 - - + -
77B TRP* 4.7 2.9 - - + -
88B SER* 3.4 25.7 + - - +
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Residues in contact with ARG 66 (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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77A TRP* 5.5 0.6 - - + +
86A TYR* 3.3 63.7 + - + +
87A ALA* 4.9 0.7 - - - -
62B HIS* 3.0 17.3 + - + +
63B ALA* 3.5 13.9 - - - +
65B VAL* 1.3 77.9 - - - +
67B LEU* 1.3 57.5 + - - +
69B ALA* 3.2 6.9 + - - +
70B GLN* 2.9 49.7 + - - +
30G T 5.4 1.0 + - - -
31G T 2.9 30.7 + - - -
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Residues in contact with LEU 67 (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 LEU* 3.6 29.6 - - + -
27B VAL* 4.1 12.1 - - + -
30B GLY* 3.6 27.8 - - - +
31B ALA 4.0 2.7 - - - -
32B PHE* 3.7 30.7 - - + +
46B VAL* 4.6 11.7 - - + -
63B ALA 2.9 17.5 + - - +
64B ALA* 3.6 5.2 - - - +
66B ARG* 1.3 74.0 - - - +
68B ALA* 1.3 65.7 + - - +
70B GLN* 3.1 18.5 + - + +
71B VAL* 3.3 16.8 + - + +
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Residues in contact with ALA 68 (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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32B PHE* 4.2 7.2 - - + -
46B VAL* 4.2 9.9 - - + -
64B ALA 2.9 17.6 + - - +
65B VAL 3.7 4.0 - - - +
67B LEU* 1.3 75.9 - - - +
69B ALA* 1.3 59.7 + - - +
71B VAL* 3.5 8.1 - - - +
72B GLY 3.3 2.4 + - - -
73B THR 2.8 36.4 + - - +
75B LEU* 3.7 36.3 - - + -
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Residues in contact with ALA 69 (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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86A TYR 3.5 24.2 - - - +
87A ALA* 3.9 10.1 - - + -
65B VAL 3.0 13.4 + - - +
66B ARG 3.5 8.3 - - - +
68B ALA* 1.3 78.9 - - - +
70B GLN* 1.3 57.6 + - - +
72B GLY* 2.9 9.7 + - - -
73B THR 4.6 2.9 - - - -
88B SER* 5.8 0.2 - - - +
89B GLY* 4.2 4.0 - - - -
90B GLN* 2.9 48.0 + - + +
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Residues in contact with GLN 70 (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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3B TRP* 5.3 9.3 - - - -
6B LEU* 3.8 37.0 + - + +
8B PRO* 3.7 17.8 - - - +
66B ARG* 2.9 44.5 + - - +
67B LEU* 3.1 14.0 + - + +
69B ALA* 1.3 77.0 - - - +
71B VAL* 1.3 61.5 + - + +
72B GLY 3.2 0.6 + - - -
90B GLN* 4.1 4.9 + - - +
303B ARG 4.8 1.2 - - - +
305B SER 4.4 13.1 + - - +
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Residues in contact with VAL 71 (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 LEU* 3.7 39.7 - - + -
7B ASN 4.5 6.1 - - - +
8B PRO* 3.2 25.5 - - + +
14B ARG* 3.2 13.2 + - - -
46B VAL* 4.0 19.5 - - + -
47B GLY* 4.0 18.5 - - - +
67B LEU* 3.3 18.1 + - + +
68B ALA 3.5 5.6 - - - +
70B GLN* 1.3 75.9 - - - +
72B GLY* 1.3 59.8 - - - +
73B THR* 3.4 18.6 - - - +
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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