Contacts of the strand formed by residues 42 - 50 (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 ARG 42 (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 2.9 12.0 + - - +
11B SER* 3.7 3.8 - - - -
12B ILE* 3.0 25.1 + - - +
37B SER* 6.4 2.7 - - - +
38B THR 4.9 4.7 - - - +
41B PHE* 1.3 74.8 - - - +
43B LEU* 1.3 67.4 + - - +
44B THR* 3.8 3.4 + - - +
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Residues in contact with LEU 43 (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* 3.5 17.0 - - + +
14B ILE* 4.1 27.4 - - + -
33B MET* 3.3 31.6 - - + +
36B PHE 5.7 2.7 - - - +
41B PHE* 3.7 31.2 - - + +
42B ARG* 1.3 79.8 - - - +
44B THR* 1.3 60.8 + - - +
45B PRO* 3.1 11.9 - - - +
289B VAL* 4.9 5.4 - - + +
292B MET* 4.5 18.8 - - + -
293B THR* 4.2 20.9 - - + +
296B PHE* 5.6 1.6 - - + -
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Residues in contact with THR 44 (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* 3.2 22.6 + - - +
12B ILE 2.9 12.5 + - - -
13B GLN* 3.5 14.3 - - + +
14B ILE* 3.0 24.3 + - - +
42B ARG* 4.3 3.1 + - - +
43B LEU* 1.3 73.3 + - - +
45B PRO* 1.3 67.1 - - + +
46B HIS* 3.6 2.3 + - + +
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Residues in contact with PRO 45 (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* 3.6 13.9 - - + +
15B GLY 5.7 0.9 - - - -
16B GLY 6.0 0.2 - - - +
29B PHE* 3.8 25.4 - - + -
33B MET* 3.6 31.2 - - + -
43B LEU 3.1 11.0 - - - +
44B THR* 1.3 88.8 - - + +
46B HIS* 1.3 59.9 + - - +
47B ILE* 3.8 15.1 + - + +
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Residues in contact with HIS 46 (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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13B GLN* 6.6 0.4 - - + -
14B ILE 3.0 16.3 + - - +
15B GLY* 4.0 4.1 - - - -
16B GLY 3.1 18.6 + - - +
44B THR* 3.6 2.9 + - + +
45B PRO* 1.3 70.1 - - - +
47B ILE* 1.3 65.3 + - - +
48B ASP* 3.6 30.3 + - - +
64B SER* 5.2 7.9 - - - -
65B GLN* 5.5 9.3 - - + +
68B ARG* 5.7 12.4 - - + +
70B VAL* 5.5 5.8 - - + -
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Residues in contact with ILE 47 (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* 3.5 10.8 - - - +
18B PHE* 4.1 14.8 - - + -
26B TYR* 3.5 45.8 - - + +
29B PHE* 4.0 9.9 - - + -
45B PRO* 3.8 28.9 + - + +
46B HIS* 1.3 76.3 + - - +
48B ASP* 1.3 72.0 + - - +
49B ASN* 3.5 24.8 + - - +
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Residues in contact with ASP 48 (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 2.8 14.5 + - - +
17B LEU* 3.7 9.1 - - + +
18B PHE 3.4 18.5 + - - -
46B HIS* 3.6 29.1 + - - +
47B ILE* 1.3 89.1 - - - +
49B ASN* 1.3 62.9 + - - +
50B LEU* 3.4 24.4 + - + +
61B ALA* 4.0 26.2 - - + +
64B SER* 4.7 7.7 + - - -
65B GLN* 4.8 6.2 - - - +
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Residues in contact with ASN 49 (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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18B PHE* 3.3 24.3 - - - +
20B ARG* 5.1 16.0 - - + +
26B TYR* 5.8 0.3 - - - -
47B ILE* 3.5 23.4 + - - +
48B ASP* 1.3 68.4 - - - +
50B LEU* 1.3 67.0 + - - +
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Residues in contact with LEU 50 (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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18B PHE 3.6 2.7 + - - +
19B PRO* 3.4 19.4 - - - +
20B ARG* 3.7 5.9 + - - -
48B ASP* 3.4 32.5 + - + +
49B ASN* 1.3 82.0 - - - +
51B GLU* 1.3 62.7 + - - +
52B VAL* 2.9 10.2 + - - -
57B ALA* 3.3 43.7 - - + +
58B VAL* 5.5 2.9 - - + +
60B ASN* 5.4 2.5 - - + -
61B ALA* 3.7 17.9 - - + +
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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