Contacts of the strand formed by residues 7 - 15 (chain D) in PDB entry 6QPA
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 ILE 7 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ASN 4.7 5.2 - - - +
6D PRO* 1.3 78.9 - - - +
8D ILE* 1.3 63.9 + - - +
9D ALA 4.1 0.6 + - - +
80D THR 3.9 0.7 - - - +
81D VAL* 3.4 4.3 - - - +
82D TRP* 2.9 40.9 + - + +
83D LYS 4.7 2.5 - - - +
84D ASP* 4.2 21.8 - - - -
85D VAL* 4.1 9.9 - - + +
118D TYR* 3.9 28.3 - - + -
119D PHE 3.7 13.5 - - - +
120D GLU* 4.4 11.2 - - + -
121D VAL 5.4 0.2 - - - +
202D PHE* 4.1 25.8 - - + -
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Residues in contact with ILE 8 (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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6D PRO 4.7 0.4 - - - +
7D ILE* 1.3 79.8 - - - +
9D ALA* 1.3 65.4 + - - +
10D ILE* 3.8 22.7 - - + -
79D TYR* 4.0 21.3 - - + -
80D THR 3.6 4.9 - - - +
81D VAL* 4.2 15.5 - - + -
118D TYR* 3.6 0.5 - - - -
119D PHE* 2.7 49.1 + - + +
121D VAL* 3.9 28.0 - - + -
197D MET* 4.0 15.5 - - + -
199D MET* 3.9 16.6 - - - -
308D TRP* 4.2 13.7 - - + -
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Residues in contact with ALA 9 (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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7D ILE 4.1 1.2 + - - -
8D ILE* 1.3 71.4 - - - +
10D ILE* 1.3 61.5 + - - +
11D ASN 3.9 0.4 - - - -
78D GLN 3.3 2.4 - - - +
79D TYR* 3.4 2.4 - - - -
80D THR* 2.8 52.2 + - - +
82D TRP* 4.3 3.0 - - + +
88D HIS* 4.0 17.7 - - + +
116D GLU* 3.8 18.6 - - + +
117D PRO 3.6 5.4 - - - +
118D TYR* 4.1 17.2 - - + -
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Residues in contact with ILE 10 (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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8D ILE* 3.8 7.2 - - + -
9D ALA* 1.3 75.2 - - - +
11D ASN* 1.3 62.4 + - - +
12D MET* 3.3 20.8 + - + +
77D PHE* 3.8 22.9 - - + -
78D GLN 3.4 2.5 - - - +
79D TYR* 3.6 34.8 - - + -
116D GLU* 3.3 3.4 - - - -
117D PRO* 3.1 33.0 + - - +
119D PHE* 3.6 32.8 - - + -
199D MET* 3.8 25.4 - - + -
254D LEU* 4.0 9.0 - - + -
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Residues in contact with ASN 11 (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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9D ALA 3.9 0.6 - - - -
10D ILE* 1.3 70.5 - - - +
12D MET* 1.3 61.2 + - - +
13D ALA* 4.4 5.7 - - - +
76D MET 3.5 2.3 - - - +
77D PHE* 3.2 5.2 - - - -
78D GLN* 2.8 59.4 + - + +
92D HIS* 6.1 1.2 + - - -
114D PRO* 3.4 23.4 - - - +
115D TRP 3.8 2.9 - - - -
116D GLU* 3.7 23.0 + - - +
208D GLY* 3.5 24.2 + - - -
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Residues in contact with MET 12 (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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10D ILE* 3.6 23.6 - - + +
11D ASN* 1.3 72.6 + - - +
13D ALA* 1.3 61.4 + - - +
76D MET 3.8 2.5 - - - -
77D PHE* 3.7 30.1 - - + -
113D GLY* 3.9 2.9 - - - -
114D PRO* 3.3 4.3 - - - +
115D TRP* 2.8 45.1 + - + +
117D PRO* 4.0 19.1 - - + -
119D PHE* 3.8 19.7 - - + -
252D GLN* 4.5 8.5 - - - +
254D LEU* 3.8 28.9 - - + -
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Residues in contact with ALA 13 (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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11D ASN* 4.4 9.4 - - - +
12D MET* 1.3 76.3 - - - +
14D LYS* 1.3 63.1 + - - +
15D ILE* 4.4 15.0 - - + -
75D GLY* 3.5 3.8 - - - -
76D MET* 2.7 45.3 + - + +
77D PHE* 4.4 2.6 - - - -
110D VAL* 5.0 7.4 - - + -
112D GLU 3.5 12.1 - - - +
113D GLY* 4.5 0.4 - - - -
114D PRO* 4.5 9.0 - - + -
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Residues in contact with LYS 14 (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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13D ALA* 1.3 77.2 - - - +
15D ILE* 1.3 55.7 + - - +
50D GLN* 4.4 7.5 + - - -
73D PRO* 3.7 29.0 + - + +
74D MET 3.4 4.2 - - - +
75D GLY* 4.4 7.9 - - - +
77D PHE* 5.8 3.1 - - + -
110D VAL* 3.7 1.9 - - - -
111D ILE* 2.7 31.7 + - - -
112D GLU* 2.9 47.7 + - + +
297D MET* 4.4 21.2 - - - +
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Residues in contact with ILE 15 (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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13D ALA* 4.4 13.0 - - + -
14D LYS* 1.3 78.6 - - - +
16D ALA* 1.3 70.2 + - - +
21D SER* 4.6 2.2 - - - -
25D MET* 3.8 34.1 - - + -
49D LEU* 4.4 5.4 - - + -
73D PRO* 3.3 6.1 - - - +
74D MET* 3.0 47.4 + - + +
76D MET* 4.0 24.0 - - + -
109D MET* 3.1 45.3 - - + +
110D VAL* 4.5 7.2 - - + -
111D ILE* 4.2 0.4 - - - -
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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