Contacts of the helix formed by residues 1 - 15 (chain B) 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 GLY 1 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B LYS* 1.3 65.6 + - - +
3B HIS* 3.4 3.0 + - - +
4B ALA* 3.6 9.1 + - - +
5B LEU* 3.3 23.0 + - - +
45B ILE* 5.8 0.3 - - - +
48B GLN* 6.3 2.7 - - - -
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Residues in contact with LYS 2 (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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1B GLY* 1.3 73.8 - - - +
3B HIS* 1.3 56.3 + - - +
5B LEU* 3.4 4.8 + - - +
6B THR* 2.8 35.4 + - - +
69B LEU* 4.0 19.4 - - + +
72B TRP* 5.8 10.5 - - + +
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Residues in contact with HIS 3 (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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1B GLY 3.4 2.5 - - - +
2B LYS* 1.3 76.4 - - - +
4B ALA* 1.3 63.0 + - - +
6B THR* 3.3 8.3 + - - -
7B GLY* 3.0 25.9 + - - -
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Residues in contact with ALA 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY* 3.6 10.7 + - - +
2B LYS 3.5 0.2 - - - -
3B HIS* 1.3 84.5 + - - +
5B LEU* 1.3 62.4 + - - +
7B GLY* 3.4 2.0 + - - +
8B ALA* 3.1 18.5 + - - +
41B GLU* 6.3 1.8 - - + -
45B ILE* 3.6 34.8 - - + +
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Residues in contact with LEU 5 (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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1B GLY 3.3 16.2 + - - +
2B LYS* 3.7 5.4 - - - +
3B HIS 3.3 0.4 - - - -
4B ALA* 1.3 75.5 - - - +
6B THR* 1.3 68.1 + - - +
8B ALA* 3.2 1.6 + - + -
9B LEU* 2.9 47.3 + - + +
45B ILE* 3.9 25.5 - - + +
48B GLN* 5.7 8.1 - - + -
49B LEU* 3.7 32.3 - - + -
65B GLY 4.2 10.1 - - - +
68B LYS* 4.7 18.2 - - + +
69B LEU* 4.1 21.5 - - + -
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Residues in contact with THR 6 (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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2B LYS* 2.8 23.2 + - - +
3B HIS* 3.3 8.7 + - + -
5B LEU* 1.3 75.8 - - - +
7B GLY* 1.3 57.0 + - - +
9B LEU* 3.4 1.9 + - - +
10B GLY* 2.9 27.4 + - - -
69B LEU* 3.6 26.2 - - + +
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Residues in contact with GLY 7 (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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3B HIS* 3.0 15.8 + - - -
4B ALA* 3.4 4.0 + - - -
5B LEU 3.2 0.4 - - - -
6B THR* 1.3 78.1 - - - +
8B ALA* 1.3 55.7 + - - +
10B GLY* 3.4 2.4 + - - -
11B ASN* 2.9 38.5 + - - +
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Residues in contact with ALA 8 (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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4B ALA 3.1 16.5 + - - +
5B LEU* 3.8 3.1 - - + +
7B GLY* 1.3 73.9 - - - +
9B LEU* 1.3 67.5 + - + +
11B ASN* 3.4 4.7 + - - +
12B MET* 3.1 30.2 + - - +
42B LEU* 5.4 0.9 - - + -
45B ILE* 4.1 15.0 - - + -
49B LEU* 6.1 0.2 - - + -
109B PHE* 4.1 17.9 - - + -
113B CYS* 3.7 24.5 - - + -
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Residues in contact with LEU 9 (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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5B LEU* 2.9 38.1 + - + +
6B THR* 3.9 3.4 - - - +
8B ALA* 1.3 74.2 - - + +
10B GLY* 1.3 65.5 + - - +
12B MET* 3.4 27.9 + - + +
13B LYS* 3.1 21.5 + - - +
49B LEU* 4.6 11.4 - - + -
62B LEU* 5.3 5.4 - - + +
65B GLY 4.3 9.6 - - - +
66B TYR* 3.7 51.1 + - + +
69B LEU* 3.9 26.5 - - + -
92B ILE* 5.2 1.2 - - + +
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Residues in contact with GLY 10 (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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6B THR 2.9 15.6 + - - -
7B GLY* 3.7 4.3 - - - -
9B LEU* 1.3 75.7 - - - +
11B ASN* 1.3 57.8 + - - +
13B LYS* 3.0 14.0 + - - +
14B LYS* 3.0 33.3 + - - +
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Residues in contact with ASN 11 (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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7B GLY* 2.9 25.4 + - - +
8B ALA* 3.9 7.2 - - - +
9B LEU 3.3 0.2 - - - -
10B GLY* 1.3 74.3 - - - +
12B MET* 1.3 64.5 + - - +
14B LYS* 3.5 24.1 + - - +
15B PHE* 3.1 22.5 + - - +
112B VAL* 4.0 8.4 - - - +
113B CYS* 3.9 28.5 + - - -
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Residues in contact with MET 12 (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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8B ALA 3.1 18.4 + - - +
9B LEU* 3.7 34.3 - - + +
11B ASN* 1.3 73.9 - - - +
13B LYS* 1.3 61.7 + - - +
15B PHE* 3.2 15.8 + - - +
49B LEU* 5.0 0.7 - - + -
62B LEU* 4.2 13.2 - - + -
91B HIS* 3.4 12.9 + - - -
92B ILE* 3.9 39.3 - - + -
96B VAL* 4.3 17.5 - - + +
104B ILE* 5.0 3.1 - - - -
109B PHE* 4.0 32.1 - - + -
112B VAL* 3.8 14.8 - - + -
113B CYS* 3.7 13.5 - - - -
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Residues in contact with LYS 13 (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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9B LEU 3.1 12.5 + - - +
10B GLY* 3.0 14.2 + - - +
12B MET* 1.3 75.7 - - - +
14B LYS* 1.3 67.1 + - + +
16B GLN* 3.8 7.6 + - - -
66B TYR* 4.6 7.0 - - - +
84B GLN* 5.0 2.0 - - - +
88B GLU* 3.4 38.2 + - - +
91B HIS* 3.5 21.1 + - + -
92B ILE* 5.1 1.7 - - - +
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Residues in contact with LYS 14 (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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10B GLY* 3.0 16.1 + - - +
11B ASN* 3.9 25.9 + - - +
13B LYS* 1.3 78.2 - - + +
15B PHE* 1.3 63.6 + - - +
16B GLN* 3.3 15.4 + - - +
199B GOL 3.4 8.0 + - - -
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Residues in contact with PHE 15 (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 ASN 3.1 14.3 + - - +
12B MET 3.4 12.3 - - - +
13B LYS 3.2 1.8 - - - -
14B LYS* 1.3 74.5 - - - +
16B GLN* 1.3 66.1 + - - +
17B SER* 4.7 2.7 - - - -
18B SER 5.9 0.2 - - - -
26B MET* 3.4 28.7 - - + -
91B HIS* 2.7 32.4 + - - -
95B SER* 3.5 36.8 + - - -
96B VAL* 4.3 2.0 - - + -
98B PHE* 3.8 18.8 - + - -
112B VAL* 3.8 37.0 - - + -
116B LYS* 5.2 2.7 - - - -
199B GOL 2.8 43.1 - - - -
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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