Contacts of the strand formed by residues 11 - 19 (chain B) in PDB entry 3KG2
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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ASN* 1.3 71.6 - - - +
12B ILE* 1.3 62.2 + - - +
13B GLN* 3.7 4.0 + - - +
42B ARG* 3.7 5.2 - - - -
44B THR* 3.2 21.5 + - - +
71B TYR* 4.4 9.4 + - - -
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Residues in contact with ILE 12 (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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10B ASN* 5.0 2.0 - - + -
11B SER* 1.3 73.7 + - - +
13B GLN* 1.3 61.5 + - - +
14B ILE* 3.6 14.7 + - + +
41B PHE* 3.9 27.1 - - + -
42B ARG 3.0 14.4 + - - +
43B LEU* 3.5 11.5 - - + -
44B THR* 2.9 24.0 + - - -
71B TYR* 3.7 31.0 - - + -
296B PHE* 3.6 33.4 - - + +
306B ILE* 6.3 2.9 - - + -
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Residues in contact with GLN 13 (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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11B SER* 3.7 5.0 + - - +
12B ILE* 1.3 72.7 - - - +
14B ILE* 1.3 61.9 + - - +
44B THR* 3.5 17.9 - - + +
46B HIS* 6.6 0.2 - - + -
68B ARG 5.4 2.7 - - - +
69B GLY 4.3 15.0 - - - +
70B VAL* 3.4 8.2 - - + -
71B TYR* 3.0 37.6 + - + -
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Residues in contact with ILE 14 (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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12B ILE* 4.1 18.4 - - + +
13B GLN* 1.3 81.2 - - - +
15B GLY* 1.3 64.5 + - - +
29B PHE* 4.6 18.4 - - + -
33B MET* 5.1 1.8 - - - -
43B LEU* 4.1 27.6 - - + -
44B THR 3.0 11.8 + - - +
45B PRO* 3.9 10.5 - - + -
46B HIS* 3.0 28.8 + - - +
70B VAL* 3.8 6.6 - - - +
72B ALA* 3.3 22.0 - - + +
74B PHE* 5.8 0.7 - - + -
292B MET* 3.7 32.5 - - + -
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Residues in contact with GLY 15 (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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14B ILE* 1.3 78.6 - - - +
16B GLY* 1.3 58.3 + - - -
17B LEU* 4.2 0.4 - - - -
29B PHE* 5.6 1.1 - - - -
45B PRO* 5.7 0.4 - - - -
46B HIS* 4.0 6.3 - - - -
65B GLN* 4.6 11.7 - - - -
70B VAL* 3.8 11.2 - - - +
72B ALA 2.9 13.6 + - - +
73B ILE* 4.2 11.4 - - - -
74B PHE* 2.8 29.0 + - - +
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Residues in contact with GLY 16 (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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15B GLY* 1.3 74.3 - - - -
17B LEU* 1.3 64.9 + - - +
18B PHE* 3.6 19.1 + - - -
29B PHE* 5.5 2.7 - - - -
45B PRO* 6.1 0.2 - - - -
46B HIS 3.1 12.9 + - - +
47B ILE* 3.5 10.3 - - - -
48B ASP* 2.8 30.5 + - - +
74B PHE* 3.1 7.0 - - - -
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Residues in contact with LEU 17 (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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15B GLY* 4.6 1.3 - - - -
16B GLY* 1.3 78.6 - - - +
18B PHE* 1.3 60.7 + - - +
19B PRO* 3.6 2.1 - - - +
48B ASP* 3.7 11.4 - - + +
58B VAL* 4.6 22.0 - - + +
61B ALA* 4.2 39.3 - - + +
62B PHE* 4.8 3.6 - - + +
65B GLN* 5.1 4.0 - - + -
73B ILE* 3.6 25.1 - - + -
74B PHE 2.9 9.1 + - - -
75B GLY* 3.1 26.0 - - - -
76B PHE* 3.3 18.7 + - - +
85B ILE* 4.6 12.3 - - + -
96B PHE* 4.6 7.0 - - + -
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Residues in contact with PHE 18 (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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16B GLY* 3.8 19.5 - - - -
17B LEU* 1.3 76.7 - - - +
19B PRO* 1.3 69.7 - - + +
20B ARG 3.5 0.2 + - - -
22B ALA* 4.4 9.0 - - + +
25B GLU 4.0 6.5 - - - -
26B TYR* 3.7 50.0 - + + -
29B PHE* 3.4 22.7 - + + -
47B ILE* 4.1 12.6 - - + -
48B ASP 3.4 6.6 + - - -
49B ASN* 3.3 38.0 - - - +
50B LEU 3.6 3.0 + - - -
74B PHE* 3.3 39.0 - + - -
76B PHE* 3.9 13.7 - + - -
285B THR* 4.4 0.7 - - + -
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Residues in contact with PRO 19 (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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17B LEU 3.6 3.4 - - - +
18B PHE* 1.3 84.9 - - + +
20B ARG* 1.3 68.0 + - - +
22B ALA* 3.0 29.6 + - + +
49B ASN* 5.6 0.6 - - - -
50B LEU 3.4 11.2 - - - +
52B VAL* 3.7 37.5 - - + +
76B PHE* 3.4 35.9 - - + -
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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