Contacts of the strand formed by residues 84 - 90 (chain D) in PDB entry 3Q2P
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 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D PHE* 3.3 32.1 + - - -
14D ASN* 4.1 12.7 + - - +
15D LEU* 3.4 41.9 - - - +
18D PHE* 3.4 42.6 - - + +
75D ILE* 4.6 0.4 - - + -
76D SER 3.1 9.2 - - - +
77D GLU* 2.7 30.8 + - + +
82D ARG 4.0 6.9 + - - +
83D GLY* 1.3 76.8 - - - +
85D LYS* 1.3 74.0 + - - +
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Residues in contact with LYS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.8 7.0 - - - -
22D GLU* 6.0 0.2 - - - -
75D ILE* 3.3 4.5 - - - +
76D SER* 2.9 45.3 + - - +
83D GLY 5.6 1.1 - - - +
84D ARG* 1.3 81.5 + - - +
86D LEU* 1.3 62.9 + - - +
87D LEU* 3.4 11.5 + - + -
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.9 8.8 - - + -
19D ALA* 3.7 27.4 - - + +
22D GLU* 3.8 28.2 + - + +
23D GLU* 3.9 10.1 - - - +
26D ILE* 4.2 15.5 - - + -
73D ALA* 4.2 12.8 - - + -
74D ASP 3.5 9.9 - - - +
75D ILE* 4.4 2.7 - - + +
85D LYS* 1.3 71.7 - - - +
87D LEU* 1.3 65.0 + - - +
88D ARG 3.4 27.1 - - - +
89D PHE* 3.9 22.0 - - + -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 4.1 13.2 - - - +
74D ASP* 2.7 39.1 + - - +
76D SER* 3.6 35.7 - - - +
85D LYS* 3.9 15.9 - - + +
86D LEU* 1.3 79.9 - - - +
88D ARG* 1.3 83.6 + - + +
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PRO* 3.6 37.4 - - - +
95C PRO* 3.8 21.9 + - - +
59D GLU* 5.9 1.0 + - - -
72D ARG* 4.4 1.6 - - - +
73D ALA* 3.3 3.3 - - - -
74D ASP* 2.7 52.9 + - + -
86D LEU* 3.4 7.5 - - - +
87D LEU* 1.3 95.1 + - + +
89D PHE* 1.3 60.6 + - - +
90D ASN* 4.4 14.1 - - - +
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Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA* 4.1 28.7 - - + -
20D VAL* 4.4 13.9 - - + -
23D GLU* 3.3 42.1 - - + +
28D GLN* 4.3 4.5 - - - +
29D TYR* 3.6 20.7 + + - -
32D LEU* 4.0 11.9 - - + -
64D VAL* 5.0 5.8 - - + -
66D ALA* 5.1 0.9 - - + -
71D PHE* 3.4 41.5 - + + -
72D ARG 3.4 2.9 - - - -
73D ALA* 3.7 25.4 - - + -
86D LEU* 3.9 11.2 - - + +
88D ARG* 1.3 74.4 - - - +
90D ASN* 1.3 73.4 + - - +
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Residues in contact with ASN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PRO* 5.0 14.8 - - - +
28D GLN* 4.7 4.9 + - - +
29D TYR* 3.4 9.7 + - - -
71D PHE* 3.4 5.9 - - - -
72D ARG* 2.9 37.6 + - + +
88D ARG* 4.3 16.4 - - - +
89D PHE* 1.3 88.2 - - - +
91D GLY* 1.3 58.7 + - - +
93D VAL* 3.6 8.4 - - + +
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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