Contacts of the helix formed by residues 10 - 20 (chain A) in PDB entry 3KHR
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 TYR 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASP* 1.3 85.6 - - + +
11A PHE* 1.3 65.1 + - - +
12A TYR 3.6 0.9 - - - -
13A ALA* 3.2 5.7 + - + -
14A GLN* 2.9 56.6 + - + +
17A GLU* 3.1 31.6 + - - -
24A LYS* 4.3 10.9 + - - -
45A THR* 4.7 1.3 - - - +
46A ALA 3.9 9.0 - - - +
47A ASN* 3.5 21.1 - - + -
48A TYR* 3.8 21.3 - + + -
49A GLU* 5.9 0.7 - - - -
51A ARG* 3.5 18.2 - - - +
139A THR* 4.7 4.3 + - - -
160A PRO* 5.3 2.7 - - + -
414A TTP 2.9 32.7 + - - -
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Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.7 30.3 - + + -
9A ASP 2.9 8.1 + - - -
10A TYR* 1.3 70.4 - - - +
12A TYR* 1.3 80.4 + + - +
14A GLN* 3.2 1.4 + - + +
15A VAL* 3.0 37.5 + - + +
81A TYR* 3.6 33.9 - - + -
84A VAL* 3.8 20.2 - - + -
85A SER* 3.9 6.1 - - - -
88A ILE* 4.5 3.4 - - + -
104A ILE* 4.1 19.3 - - + -
105A ASP* 3.7 33.7 - - + +
138A ILE* 4.7 9.6 - - + -
414A TTP 2.9 17.8 + - - +
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Residues in contact with TYR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR 3.3 0.2 + - - -
11A PHE* 1.3 88.6 - + - +
13A ALA* 1.3 62.9 + - - +
15A VAL 3.4 1.6 + - - -
16A GLU* 3.2 24.6 + - - +
30A VAL* 4.1 8.7 - - + -
44A ALA* 4.1 7.6 - - + -
45A THR* 3.8 9.6 - - + -
76A MET* 3.6 30.5 - - + -
78A LYS* 3.4 27.2 + - + +
81A TYR* 3.4 55.5 - + + -
104A ILE* 4.0 18.1 - - + +
414A TTP 3.2 45.8 + - + -
815D DDG 5.8 1.6 + - - -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR* 3.2 14.0 + - + +
12A TYR* 1.3 78.6 - - - +
14A GLN* 1.3 57.7 + - - +
16A GLU* 3.1 6.2 + - - +
17A GLU* 2.9 29.7 + - - +
28A VAL* 4.1 13.8 - - + +
30A VAL* 3.7 21.4 - - + +
45A THR* 3.8 4.7 - - + +
46A ALA* 4.1 5.2 - - - -
47A ASN* 3.7 28.0 - - + +
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Residues in contact with GLN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 2.8 31.5 - - - +
10A TYR* 2.9 38.7 + - + +
11A PHE* 3.6 3.8 - - - +
13A ALA* 1.3 74.2 - - - +
15A VAL* 1.3 65.1 + - - +
17A GLU* 3.1 7.5 + - + +
18A VAL* 2.9 24.2 + - + +
24A LYS* 6.0 1.4 - - - +
137A LYS 3.7 6.1 + - - -
138A ILE* 3.4 23.9 - - + +
139A THR* 2.7 58.1 + - - +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.0 48.4 + - + +
12A TYR 3.6 7.9 - - - +
14A GLN* 1.3 73.7 - - - +
16A GLU* 1.3 57.8 + - - +
18A VAL* 3.1 7.0 + - + +
19A LEU* 2.9 47.3 + - + +
80A VAL* 4.2 7.2 - - + -
81A TYR* 3.7 25.6 - - + -
84A VAL* 4.2 24.9 - - + -
138A ILE* 4.4 7.9 - - + -
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR 3.2 13.9 + - - +
13A ALA* 3.1 10.6 + - - +
15A VAL* 1.3 75.3 - - - +
17A GLU* 1.3 57.0 + - - +
19A LEU* 3.4 5.3 + - - +
20A ASN* 2.8 27.0 + - - +
23A LEU* 3.7 10.8 - - + +
28A VAL* 4.9 1.6 - - + -
30A VAL* 4.4 7.9 - - + -
74A LEU* 3.7 37.0 - - + +
75A PRO 4.5 1.6 - - - +
77A ARG* 2.9 41.9 + - - +
81A TYR* 2.6 31.3 + - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR* 3.1 36.5 + - - -
13A ALA 2.9 14.7 + - - +
14A GLN* 3.1 7.5 + - + +
16A GLU* 1.3 74.4 - - - +
18A VAL* 1.3 65.1 + - - +
20A ASN 3.0 24.6 - - - -
21A PRO* 3.1 10.4 - - - +
23A LEU* 4.0 16.6 - - + +
24A LYS* 3.8 37.3 + - + +
25A GLY 4.5 1.8 + - - -
28A VAL* 4.6 4.3 - - + -
47A ASN* 2.9 29.1 + - - +
49A GLU* 4.6 1.6 - - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLN* 2.9 21.6 + - + +
15A VAL* 3.1 8.5 + - + +
17A GLU* 1.3 77.2 - - - +
19A LEU* 1.3 71.5 + - + +
21A PRO* 3.7 13.3 - - - +
136A GLU 4.2 6.3 - - - +
137A LYS* 3.4 45.3 - - + +
138A ILE* 3.7 14.6 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 2.9 38.9 + - + +
16A GLU* 3.8 7.2 - - - +
18A VAL* 1.3 85.4 - - + +
20A ASN* 1.3 61.0 + - + +
21A PRO* 3.8 4.4 - - - +
77A ARG* 3.6 29.2 - - - +
80A VAL* 3.9 16.2 - - + -
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU* 2.8 12.4 + - - +
17A GLU 3.0 6.8 - - - +
19A LEU* 1.3 80.7 - - + +
21A PRO* 1.4 58.2 - - - +
22A SER* 2.5 31.8 + - - -
23A LEU* 3.0 44.5 + - + +
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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