Contacts of the strand formed by residues 9 - 19 (chain D) in PDB entry 3BXB
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 MET 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LEU 4.2 4.7 - - - +
5D ILE* 4.0 12.8 - - + -
6D THR* 3.3 36.1 - - - +
8D ASN* 1.3 71.9 - - - +
10D HIS* 1.3 62.5 + - - +
31D GLU* 3.0 8.9 - - - +
32D GLY 3.0 31.9 + - - -
34D PRO* 3.4 25.4 - - + -
69D PHE* 3.7 17.4 - - + -
110D LEU* 4.0 12.1 - - + -
113D GLY 3.3 27.1 - - - +
115D LEU* 3.8 31.6 - - + +
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Residues in contact with HIS 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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9D MET* 1.3 81.8 - - - +
11D MET* 1.3 64.8 + - - +
12D LYS* 6.1 1.3 - - - +
30D GLY 3.4 6.1 + - - +
31D GLU* 3.5 27.4 + - + +
113D GLY 4.9 3.4 + - - +
114D CYS* 3.8 18.4 - - + -
115D LEU* 3.1 21.7 + - - +
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Residues in contact with MET 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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10D HIS* 1.3 77.3 - - - +
12D LYS* 1.3 65.8 + - - +
29D GLU* 3.3 6.1 - - - +
30D GLY 2.9 38.6 + - - +
31D GLU 3.7 19.1 - - - +
39D GLN* 3.6 23.3 - - + +
40D THR 3.3 26.0 - - - +
41D MET* 3.3 29.8 - - + -
66D SER* 3.5 7.0 - - - -
69D PHE* 3.4 24.0 - - + -
114D CYS* 3.8 1.6 - - - -
115D LEU* 3.0 21.1 - - + +
117D TYR* 4.0 7.9 - - + -
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Residues in contact with LYS 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 HIS* 6.1 1.8 - - - +
11D MET* 1.3 78.0 + - - +
13D LEU* 1.3 56.2 + - - +
28D SER 3.5 4.9 - - - +
29D GLU* 3.1 34.7 + - + +
114D CYS* 3.9 15.9 - - - -
115D LEU 2.8 7.0 + - - +
116D ILE* 3.3 23.6 - - + +
117D TYR* 2.7 34.1 + - - +
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Residues in contact with LEU 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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12D LYS* 1.3 76.9 - - - +
14D TYR* 1.3 64.0 + - - +
15D MET* 3.8 18.6 - - + +
26D CYS 4.5 2.5 - - - +
27D THR* 3.4 8.8 - - - +
28D SER* 2.8 49.0 + - - +
41D MET* 4.5 1.6 - - + -
61D SER 4.1 0.2 - - - +
62D PHE* 3.5 65.1 - - + +
106D GLN* 5.6 0.2 - - - +
117D TYR* 3.4 19.1 - - + -
119D VAL* 3.7 25.6 - - + -
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Residues in contact with TYR 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 LEU* 1.3 77.0 - - - +
15D MET* 1.3 76.7 + - - +
16D GLU* 2.9 34.8 + - + -
25D LYS* 2.8 44.0 + - + -
26D CYS 3.6 9.2 - - - -
27D THR* 4.4 11.4 - - + -
46D VAL* 5.8 1.3 - - + -
116D ILE* 6.1 0.2 - - - +
117D TYR 2.8 13.9 + - - +
118D ASN* 3.3 30.3 - - - +
119D VAL* 2.9 25.6 + - - +
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Residues in contact with MET 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 LEU* 3.8 12.1 - - + -
14D TYR* 1.3 83.2 - - - +
16D GLU* 1.3 66.7 + - - +
24D PHE* 3.7 25.8 - - - -
25D LYS* 3.4 2.6 - - - -
26D CYS* 2.8 39.9 + - + +
58D LEU* 4.4 5.4 - - + -
61D SER* 3.8 30.3 - - - +
62D PHE* 3.5 43.5 - - + -
119D VAL* 3.1 19.1 - - + +
121D ILE* 3.9 20.2 - - + -
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Residues in contact with GLU 16 (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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14D TYR* 2.9 35.5 + - + +
15D MET* 1.3 81.3 - - - +
17D GLY* 1.3 61.8 + - - +
23D HIS* 4.4 11.7 + - - +
24D PHE* 3.4 13.9 - - - +
25D LYS* 4.0 12.0 + - + -
119D VAL 3.1 7.9 + - - +
120D LYS* 3.2 31.7 - - + +
121D ILE* 2.9 23.9 + - - +
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Residues in contact with GLY 17 (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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16D GLU* 1.3 79.0 - - - +
18D THR* 1.3 66.4 + - - -
23D HIS* 3.3 7.0 - - - -
24D PHE* 2.9 43.7 + - - +
120D LYS* 6.0 0.2 - - - -
121D ILE* 3.2 15.5 - - - -
122D ARG* 5.0 5.2 - - - -
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Residues in contact with THR 18 (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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105B THR* 4.7 8.4 + - + +
120B LYS* 5.4 4.7 + - - +
17D GLY* 1.3 77.2 + - - -
19D VAL* 1.3 62.7 + - - +
20D ASN 4.6 0.4 - - - +
21D ASN* 3.6 21.8 - - - +
22D HIS 3.3 27.4 - - - +
23D HIS* 4.0 13.2 - - - +
24D PHE* 3.7 2.3 - - - -
121D ILE 3.3 6.3 + - - +
122D ARG* 3.3 29.1 + - - +
123D GLY 2.6 32.3 + - - +
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Residues in contact with VAL 19 (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 THR* 1.3 80.5 - - - +
20D ASN* 1.3 76.9 + - + +
21D ASN 3.4 0.9 - - - -
22D HIS* 3.2 22.9 + - - +
24D PHE* 4.0 8.3 - - + -
53D PHE* 3.6 47.1 - - + -
57D ILE* 4.1 17.0 - - + -
58D LEU* 4.7 0.4 - - + -
102D LEU* 4.4 7.9 - - + -
121D ILE* 4.5 1.6 - - + -
123D GLY* 3.2 10.5 - - - +
126D PHE* 3.8 28.5 - - + -
133D MET* 4.7 2.6 - - - +
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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