Contacts of the helix formed by residues 3 - 15 (chain A) in PDB entry 3KHE
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 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ALA* 1.3 81.6 + - + +
5A LEU* 3.2 8.8 - - - +
6A THR* 3.1 22.3 + - - +
7A GLY* 3.0 23.9 + - - -
69A LEU* 5.6 2.2 - - - +
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Residues in contact with ALA 4 (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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3A HIS* 1.3 90.1 + - + +
5A LEU* 1.3 64.0 + - - +
7A GLY* 3.2 3.5 + - - +
8A ALA 3.0 19.2 + - - -
41A GLU* 6.3 1.6 - - + -
45A ILE* 3.5 30.9 - - + +
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Residues in contact with LEU 5 (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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3A HIS 3.2 5.8 - - - +
4A ALA* 1.3 79.1 - - - +
6A THR* 1.3 56.4 + - - +
8A ALA* 3.3 1.2 + - - -
9A LEU* 2.9 50.9 + - + +
45A ILE* 4.0 26.6 - - + +
48A GLN* 5.6 7.4 - - + -
49A LEU* 3.7 31.2 - - + -
65A GLY* 4.2 12.8 - - - +
68A LYS* 5.5 6.3 - - + -
69A LEU* 4.0 27.4 - - + +
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Residues in contact with THR 6 (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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3A HIS* 3.1 23.2 + - - -
5A LEU* 1.3 79.4 - - - +
7A GLY* 1.3 52.1 + - - +
9A LEU* 3.4 1.4 + - - +
10A GLY* 2.8 33.4 + - - -
69A LEU* 3.5 33.9 - - + +
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Residues in contact with GLY 7 (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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3A HIS 3.0 13.5 + - - -
4A ALA* 3.2 4.2 + - - -
6A THR* 1.3 76.4 - - - +
8A ALA* 1.3 56.0 + - - +
10A GLY* 3.4 1.8 + - - -
11A ASN* 2.9 39.4 + - - -
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Residues in contact with ALA 8 (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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4A ALA 3.0 14.8 + - - +
5A LEU 4.1 2.5 - - - +
7A GLY* 1.3 72.2 - - - +
9A LEU* 1.3 64.5 + - + +
11A ASN* 3.4 5.5 + - - +
12A MET* 3.0 32.8 + - - +
42A LEU* 4.8 2.9 - - + -
45A ILE* 4.2 15.3 - - + -
109A PHE* 4.0 18.4 - - + -
113A CYS* 3.6 27.4 - - + -
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Residues in contact with LEU 9 (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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5A LEU* 2.9 41.4 + - + +
6A THR 3.9 2.7 - - - +
8A ALA* 1.3 73.3 - - + +
10A GLY* 1.3 60.0 + - - +
12A MET* 3.3 26.7 + - + +
13A LYS* 2.9 27.1 + - - +
49A LEU* 4.4 13.2 - - + -
62A LEU* 5.4 2.2 - - + +
65A GLY* 4.0 19.7 - - - +
66A TYR* 3.1 44.4 + - + +
69A LEU* 3.6 28.0 - - + -
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Residues in contact with GLY 10 (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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6A THR 2.8 18.5 + - - -
7A GLY* 3.6 2.5 - - - -
9A LEU* 1.3 74.8 - - - +
11A ASN* 1.3 61.6 + - - +
13A LYS* 3.1 14.7 + - - +
14A LYS* 3.1 35.0 + - - +
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Residues in contact with ASN 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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7A GLY* 2.9 32.7 + - - +
8A ALA* 3.9 5.6 - - - +
10A GLY* 1.3 73.1 - - - +
12A MET* 1.3 62.4 + - - +
14A LYS* 3.5 17.5 + - - +
15A PHE* 3.1 24.4 + - - +
112A VAL* 4.0 18.8 - - - +
113A CYS* 3.8 19.9 + - - -
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Residues in contact with MET 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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8A ALA 3.0 17.9 + - - +
9A LEU* 3.3 32.7 + - + +
11A ASN* 1.3 71.9 - - - +
13A LYS* 1.3 65.0 + - - +
15A PHE* 3.4 10.4 + - - +
49A LEU* 4.8 1.1 - - + -
62A LEU* 3.9 24.2 - - + -
91A HIS* 3.1 14.1 + - - -
92A ILE* 3.9 38.3 - - + +
96A VAL* 4.4 17.0 - - + +
104A ILE* 4.9 3.4 - - - -
109A PHE* 4.2 27.1 - - + -
112A VAL* 3.9 14.8 - - + -
113A CYS* 3.7 13.2 - - - -
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Residues in contact with LYS 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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9A LEU 2.9 10.8 + - - +
10A GLY* 3.2 13.2 - - - +
12A MET* 1.3 77.0 - - - +
14A LYS* 1.3 60.9 + - + +
16A GLN* 4.0 3.6 + - - -
66A TYR* 3.6 39.3 + - - +
88A GLU* 3.2 40.3 + - + +
91A HIS* 2.4 30.4 + - + -
92A ILE* 4.9 1.1 - - + +
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Residues in contact with LYS 14 (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 GLY* 3.1 20.7 + - - +
11A ASN* 3.5 18.3 + - - +
13A LYS* 1.3 81.6 - - + +
15A PHE* 1.3 62.4 + - - +
16A GLN* 3.3 18.4 + - - +
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Residues in contact with PHE 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 ASN 3.1 17.6 + - - +
12A MET 3.7 8.1 - - - +
13A LYS 3.2 2.4 - - - -
14A LYS* 1.3 74.2 - - - +
16A GLN* 1.3 77.7 + - - +
17A SER* 4.6 2.5 - - - -
18A SER* 5.8 2.0 - - - -
26A MET* 3.6 27.8 - - + -
91A HIS* 3.0 24.9 - - - -
95A SER* 3.5 36.9 + - - -
96A VAL* 4.0 2.0 - - + -
98A PHE* 3.6 16.8 - + - -
112A VAL* 3.5 44.6 - - + -
116A LYS* 5.3 2.7 - - - -
186A ILE* 6.5 0.7 - - + -
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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