Contacts of the strand formed by residues 11 - 20 (chain C) in PDB entry 1KCG
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 HIS 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C ASP* 3.0 31.3 + - - -
10C ALA* 1.3 74.9 + - - +
12C SER* 1.3 60.3 + - - +
37C ASP* 2.3 41.5 + - - +
108C GLU* 3.2 4.3 - - - +
109C CYS 2.8 32.1 + - - -
174C LEU* 3.6 7.7 - - + +
178C LEU* 3.3 33.5 - - + +
181C ARG* 4.1 19.0 + - - -
999C GSH 3.6 31.3 + - + -
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Residues in contact with SER 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C HIS* 1.3 75.0 - - - +
13C LEU* 1.3 67.0 + - - +
14C TRP* 3.7 20.0 + - - -
35C GLN 4.5 0.2 - - - -
36C VAL* 4.2 1.7 - - - +
37C ASP* 2.8 31.2 + - - -
38C GLN* 3.7 19.1 + - - +
107C CYS 3.4 5.4 - - - -
108C GLU* 3.5 26.0 - - - -
174C LEU* 4.4 5.8 - - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER* 1.3 76.7 - - - +
14C TRP* 1.3 67.9 + - - +
15C TYR* 3.7 31.9 - - + +
35C GLN 3.4 9.4 - - - +
36C VAL* 3.6 34.1 - - + -
41C PHE* 4.5 2.7 - - + -
105C MET 3.9 0.7 - - - +
106C SER* 3.3 4.3 - - - -
107C CYS* 3.0 34.1 + - - -
170C CYS* 3.4 28.5 - - - +
173C TRP* 4.2 7.9 - - + -
174C LEU* 3.7 22.7 - - + +
177C PHE* 4.3 10.8 - - + -
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Residues in contact with TRP 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER* 3.7 19.5 + - - -
13C LEU* 1.3 85.7 - - - +
15C TYR* 1.3 63.8 + - - +
16C ASN* 4.1 6.1 - - - +
33C GLN 3.7 0.5 - - - +
34C SER* 3.1 8.3 - - - -
35C GLN* 2.9 74.6 + - - +
38C GLN* 3.5 48.2 - - + -
104C ARG* 3.4 43.7 - - - +
105C MET 3.7 2.9 - - - -
106C SER* 3.5 15.5 - - - -
108C GLU* 3.7 20.0 + - - -
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Residues in contact with TYR 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.7 35.2 - - + +
14C TRP* 1.3 75.2 - - - +
16C ASN* 1.3 62.1 + - - +
17C PHE* 3.8 20.5 + - + -
32C VAL* 4.6 2.7 - - + -
33C GLN 3.5 1.6 - - - -
34C SER* 3.0 34.5 - - - -
41C PHE* 3.9 2.1 - + - -
70C GLN* 2.6 32.6 + - - -
74C LEU* 3.5 25.6 - - + -
103C VAL 3.4 1.6 - - - +
104C ARG* 3.2 4.8 - - - +
105C MET* 2.9 57.9 + - + +
170C CYS* 4.3 3.6 - - - -
173C TRP* 3.4 29.8 - + - -
177C PHE* 4.2 0.9 - - - -
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Residues in contact with ASN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TRP* 4.4 3.4 - - - +
15C TYR* 1.3 73.6 - - - +
17C PHE* 1.3 61.8 + - - +
18C THR* 4.7 0.7 + - - -
31C GLU 3.8 0.3 - - - +
32C VAL* 3.2 5.4 - - - -
33C GLN* 2.7 51.1 + - + +
35C GLN* 3.0 29.3 + - - +
103C VAL 3.4 3.4 - - - +
104C ARG* 3.1 39.5 + - - +
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Residues in contact with PHE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TYR* 3.9 20.0 - - + -
16C ASN* 1.3 75.1 - - - +
18C THR* 1.3 64.7 + - - +
19C ILE* 4.1 17.7 - - + -
31C GLU 3.3 4.5 - - - -
32C VAL* 3.2 30.1 - - + -
46C CYS* 4.2 8.1 - - - -
74C LEU* 3.4 44.2 - - + -
77C VAL* 3.7 33.2 - - + -
78C GLY* 4.2 9.2 - - - -
81C LEU* 4.7 2.5 - - + -
102C GLN* 3.3 5.5 - - - +
103C VAL* 2.6 51.9 + - + +
105C MET* 4.6 11.7 - - + -
119C TRP* 4.9 0.7 - + - -
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ASN 4.7 0.9 + - - -
17C PHE* 1.3 77.3 + - - +
19C ILE* 1.3 61.6 - - - +
20C ILE* 4.2 20.9 + - + +
28C GLN 5.1 0.5 - - - +
29C TRP 3.4 5.0 - - - +
30C CYS* 3.7 1.0 - - - -
31C GLU* 2.8 56.2 + - + +
33C GLN* 4.7 5.9 + - - -
100C THR* 5.5 6.1 - - + -
101C LEU 3.7 3.1 - - - -
102C GLN* 4.4 15.8 - - + +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PHE* 4.2 11.4 - - + -
18C THR* 1.3 80.5 - - - +
20C ILE* 1.3 65.6 + - - +
29C TRP* 3.2 8.3 - - + +
30C CYS* 4.7 12.1 - - - -
78C GLY* 4.4 7.6 - - - +
81C LEU* 3.2 50.5 - - + -
82C ARG* 4.0 31.2 - - + +
85C LEU* 3.4 19.8 - - + +
100C THR* 3.6 1.6 - - - -
101C LEU* 2.7 48.3 + - + +
103C VAL* 4.8 3.6 - - + -
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Residues in contact with ILE 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B GLN* 5.4 0.2 + - - -
18C THR* 4.4 16.2 - - + -
19C ILE* 1.3 80.7 - - - +
21C HIS* 1.3 64.4 + - - +
22C LEU 3.7 2.3 + - - -
23C PRO* 3.8 19.4 - - + +
27C GLN* 4.1 33.0 - - + +
28C GLN 3.5 21.1 - - - +
29C TRP* 2.9 29.8 + - - +
82C ARG* 5.1 5.4 + - - -
85C LEU* 4.1 2.5 - - - -
98C PRO* 3.9 18.6 - - + -
99C LEU 3.6 10.8 - - - +
100C THR* 3.9 20.6 - - + -
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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