Contacts of the strand formed by residues 5 - 15 (chain C) in PDB entry 1KTD
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 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C GLU* 3.0 35.5 + - + -
4C GLU* 1.3 88.7 + - - +
6C THR* 1.3 64.7 + - - +
26C PHE* 3.8 21.9 - + + -
27C ASP* 2.5 30.7 + - - +
44D PHE* 2.7 44.0 + - + +
110D TYR* 3.5 36.3 - + + -
118D VAL* 4.1 15.8 - - + +
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Residues in contact with THR 6 (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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5C HIS* 1.3 78.2 + - - +
7C ILE* 1.3 66.4 + - - +
8C ILE* 3.8 29.6 - - + -
25C ASP* 3.7 1.6 - - - +
26C PHE* 3.5 4.9 - - - -
27C ASP* 2.6 42.5 + - - +
41D GLU* 4.9 0.2 - - + -
42D CYS 3.2 11.4 - - - +
43D HIS* 3.6 28.6 + - + +
44D PHE* 4.5 0.2 - - - -
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Residues in contact with ILE 7 (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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6C THR* 1.3 75.9 - - - +
8C ILE* 1.3 71.6 + - - +
24C PHE* 3.9 33.2 - - + -
25C ASP 3.3 6.7 - - - +
26C PHE* 4.1 15.0 - - + -
31C ILE* 4.8 0.7 - - + -
40D SER 3.7 0.3 - - - +
42D CYS* 2.7 48.0 + - + +
44D PHE* 3.5 30.5 - - + -
106D CYS 4.6 0.2 - - - +
109D ASN* 4.3 5.2 - - + +
110D TYR* 4.2 11.7 - - + +
113D PHE* 3.3 32.1 - - + -
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Residues in contact with ILE 8 (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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6C THR* 3.8 17.7 - - + -
7C ILE* 1.3 85.5 - - - +
9C GLN* 1.3 73.6 + - - +
10C ALA* 3.7 9.4 + - + +
23C MET 3.6 0.7 - - - +
24C PHE* 3.2 4.6 - - - -
25C ASP* 2.6 60.1 + - + +
139C PRO* 4.6 7.6 - - + -
140C ARG 5.7 3.1 - - - +
39D LYS* 4.3 22.4 - - + +
40D SER 3.3 5.2 - - - +
41D GLU* 3.5 26.9 - - + +
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Residues in contact with GLN 9 (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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7C ILE* 5.2 0.2 - - - +
8C ILE* 1.3 72.1 - - - +
10C ALA* 1.3 60.2 + - - +
11C GLU* 2.9 24.5 + - - +
22C PHE* 3.4 24.9 - - + -
23C MET 3.4 4.9 - - - +
24C PHE* 3.3 18.1 - - + -
62C ASN* 3.4 2.0 - - - +
7D TYR* 3.0 16.5 - - - +
8D LEU* 3.0 61.5 + - + +
10D GLN* 5.4 0.2 + - - -
38D CYS* 3.6 2.3 - - - +
39D LYS* 3.3 4.2 - - - -
40D SER* 2.9 37.7 + - - +
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Residues in contact with ALA 10 (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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8C ILE* 3.7 2.6 + - + -
9C GLN* 1.3 75.0 - - - +
11C GLU* 1.3 62.2 + - - +
12C PHE* 5.6 0.9 - - + -
21C GLU* 4.4 4.2 - - - +
22C PHE* 3.5 2.1 + - - -
23C MET* 2.9 55.3 + - + +
139C PRO* 4.1 18.2 - - + -
145C PHE* 6.4 0.2 - - + -
37D TYR* 4.2 6.5 - - + -
38D CYS 3.6 4.5 - - - -
39D LYS* 4.1 17.9 - - + -
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Residues in contact with GLU 11 (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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9C GLN* 2.9 19.3 + - + +
10C ALA* 1.3 75.6 - - - +
12C PHE* 1.3 70.2 + - - +
21C GLU 3.1 16.2 - - - +
22C PHE* 3.6 12.8 - - + -
62C ASN* 2.8 39.7 + - - +
63C ILE* 5.0 1.1 - - + -
66C ASP* 2.4 29.6 - - - +
10D GLN* 3.0 22.1 - - - +
37D TYR* 3.1 4.4 - - - -
38D CYS* 2.9 39.1 + - + +
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Residues in contact with PHE 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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10C ALA* 5.6 0.4 - - + -
11C GLU* 1.3 82.5 - - - +
13C TYR* 1.3 67.0 + - - +
14C LEU* 4.4 3.8 - - + -
19C ARG* 4.1 15.5 - - + -
20C GLY* 3.3 20.0 - - - -
21C GLU* 3.2 52.4 + - + +
63C ILE* 4.2 5.5 - - - +
66C ASP* 4.0 8.7 + - - +
115C PRO* 3.6 28.3 - - + -
137C PHE* 4.3 8.3 - + + -
145C PHE* 4.0 28.0 - + - -
35D LEU* 3.5 20.2 - - + -
36D GLU 2.9 16.6 - - - +
37D TYR* 3.7 9.6 - + + -
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Residues in contact with TYR 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 PHE* 1.3 76.5 - - - +
14C LEU* 1.3 70.1 + - - +
15C LEU* 4.1 14.8 - - + -
18C LYS* 3.1 36.3 + - - +
19C ARG 3.3 21.8 - - - -
20C GLY* 4.3 0.9 - - - -
63C ILE* 4.0 20.2 - - + +
66C ASP* 4.1 8.0 - - + +
67C LYS* 3.8 66.4 + - + +
70C LEU* 3.5 20.7 - - + +
35D LEU* 3.6 2.3 - - - +
36D GLU* 2.9 28.7 + - + +
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Residues in contact with LEU 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 PHE* 4.4 4.7 - - + -
13C TYR* 1.3 76.2 - - - +
15C LEU* 1.3 64.8 + - - +
17C ASP* 3.7 13.0 - - + +
18C LYS* 2.7 31.9 + - - -
19C ARG* 2.6 26.5 + - + +
114C PRO* 3.7 20.9 - - + -
115C PRO* 4.0 16.2 - - + +
116C VAL* 3.3 39.7 - - + -
31D ARG* 5.2 0.2 - - - +
33D TRP* 4.1 5.6 - - + -
34D PHE 3.5 12.6 - - - +
35D LEU* 3.9 23.1 - - + -
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Residues in contact with LEU 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 TYR* 4.1 11.4 - - + +
14C LEU* 1.3 79.9 - - - +
16C PRO* 1.3 73.1 - - + +
17C ASP* 3.3 4.9 - - - -
18C LYS* 3.8 29.2 - - + -
70C LEU* 3.7 21.1 - - + -
71C ASP* 4.0 19.5 - - - +
74C LYS* 4.0 21.3 - - + +
33D TRP* 3.4 5.2 - - - +
34D PHE* 2.8 45.8 + - + +
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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