Contacts of the strand formed by residues 59 - 67 (chain B) in PDB entry 1KSG
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 VAL 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B LEU* 4.0 29.2 - - + -
23B ARG 3.1 19.5 - - - +
25B ALA 4.3 0.7 - - - +
31B LEU* 5.3 2.9 - - + -
53B ILE* 4.2 33.7 - - + +
56B CYS* 4.5 7.2 - - + +
57B LYS 5.4 0.2 - - - -
58B ALA* 1.3 80.5 - - - +
60B SER* 1.3 60.8 + - - +
61B ARG* 4.0 2.9 + - + +
107B SER 3.7 0.5 - - - +
108B LEU* 3.6 4.3 - - - -
109B ILE* 2.9 51.5 + - + +
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Residues in contact with SER 60 (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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37A ASN* 5.6 0.7 - - - -
39A GLU* 4.2 4.3 + - - -
21B ASN* 3.8 5.5 - - - +
23B ARG* 3.1 48.9 + - - +
25B ALA* 4.5 5.4 + - - +
59B VAL* 1.3 74.0 - - - +
61B ARG* 1.3 62.7 - - - +
62B GLU* 3.7 1.7 + - - +
106B GLN* 3.6 26.9 + - - +
107B SER 3.0 13.9 - - - -
108B LEU* 4.1 12.5 - - - +
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Residues in contact with ARG 61 (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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20B MET* 4.7 12.3 - - - -
21B ASN 3.6 5.8 - - - +
22B LEU* 3.3 27.3 - - + +
59B VAL* 4.0 5.4 + - + +
60B SER* 1.3 72.9 - - - +
62B GLU* 1.3 59.6 + - - +
63B LEU* 5.5 2.7 - - + -
78B GLN* 2.9 38.4 - - - +
80B VAL* 3.7 11.5 - - - +
88B GLU* 2.4 34.4 + - - -
90B TRP* 2.9 24.7 - - - +
105B TRP* 3.9 10.2 - - + +
106B GLN* 3.0 3.8 - - - +
107B SER* 2.9 37.0 + - - +
109B ILE* 4.9 11.3 - - + +
129B ILE* 5.1 11.6 - - - +
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Residues in contact with GLU 62 (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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34A LYS* 5.4 4.8 + - - -
53A LYS* 5.3 3.2 + - - -
19B TRP* 3.2 30.9 - - + +
20B MET* 3.3 4.5 - - - -
21B ASN* 3.0 44.4 + - - +
23B ARG* 2.6 37.8 + - - +
60B SER 4.7 0.2 - - - +
61B ARG* 1.3 75.1 - - - +
63B LEU* 1.3 67.1 + - - +
104B THR* 3.2 24.5 + - + +
105B TRP 3.2 11.2 - - - +
106B GLN* 3.8 18.2 - - + +
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Residues in contact with LEU 63 (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* 4.1 13.2 - - + -
19B TRP* 3.5 4.5 - - - -
20B MET* 3.2 47.6 - - + -
61B ARG* 5.5 1.6 - - + -
62B GLU* 1.3 79.3 - - - +
64B ASN* 1.3 59.8 + - - +
65B PHE* 4.2 6.4 + - + -
76B LEU* 3.8 16.8 - - + -
78B GLN* 4.4 3.8 - - - +
94B PHE* 6.3 0.7 - - + -
104B THR* 3.3 6.2 - - - +
105B TRP* 2.8 55.6 + - + +
131B THR* 4.1 9.0 - - + -
133B PHE* 3.6 28.7 - - + -
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Residues in contact with ASN 64 (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* 3.5 6.6 - - - +
18B ASN* 2.7 54.4 + - - +
19B TRP* 2.9 54.9 + - + +
63B LEU* 1.3 74.9 - - - +
65B PHE* 1.3 60.7 + - - +
102B THR* 3.5 18.2 - - - +
103B ASN 3.2 8.4 + - - -
104B THR* 3.5 17.7 + - - +
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Residues in contact with PHE 65 (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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50A PHE* 4.1 14.4 - + - -
15B PHE* 3.7 28.7 - + + -
16B LYS 3.2 11.2 - - - +
17B LEU* 4.2 3.6 - - + -
18B ASN* 4.0 1.3 - - - +
63B LEU* 4.9 6.7 - - + -
64B ASN* 1.3 78.8 - - - +
66B SER* 1.3 67.5 + - - +
67B SER* 5.1 1.6 - - - -
74B PHE* 3.7 24.2 - + - -
94B PHE* 4.2 20.2 - + - -
97B VAL* 4.7 8.1 - - + -
102B THR* 3.5 1.2 - - - +
103B ASN* 2.8 67.8 + - + -
105B TRP* 4.9 7.9 - - + -
133B PHE* 3.6 23.6 - + + -
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Residues in contact with SER 66 (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 GLY 4.2 2.0 - - - -
15B PHE* 3.5 6.4 - - - -
16B LYS* 2.8 38.2 + - - +
18B ASN* 2.9 24.1 + - - +
65B PHE* 1.3 75.9 - - - +
67B SER* 1.3 63.5 + - - +
101B SER 3.2 11.9 - - - -
102B THR* 3.5 15.1 + - - +
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Residues in contact with SER 67 (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 ILE 5.4 1.2 + - - -
14B GLY 3.4 8.2 + - - -
15B PHE* 4.9 5.6 - - - +
65B PHE* 5.1 3.4 - - - -
66B SER* 1.3 76.9 - - - +
68B THR* 1.3 60.4 + - - +
69B GLU* 2.8 27.2 + - - +
71B MET* 3.1 27.2 - - - +
97B VAL* 4.1 14.8 - - - -
98B ILE 3.9 1.6 - - - +
99B PRO 3.8 0.9 - - - -
100B ASN* 2.9 20.0 + - - -
101B SER* 3.1 16.3 + - - -
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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