Contacts of the helix formed by residues 2 - 16 (chain B) in PDB entry 2FAC
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 THR 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B SER* 1.3 75.5 - - - +
3B ILE* 1.3 65.5 + - - +
4B GLU* 3.3 13.1 + - - +
5B GLU* 2.9 40.5 + - - +
6B ARG* 2.9 24.2 + - - +
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Residues in contact with ILE 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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2B THR* 1.3 73.6 - - - +
4B GLU* 1.3 63.4 + - - +
6B ARG* 3.2 14.9 + - - +
7B VAL* 2.9 40.4 + - + +
50B PHE* 4.0 12.3 - - + -
69B ILE* 4.8 2.9 - - + +
72B ILE* 4.1 12.6 - - + -
73B ASN* 3.3 35.9 - - - +
76B GLN* 3.5 36.3 - - - +
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Residues in contact with GLU 4 (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 THR* 3.2 11.3 + - - +
3B ILE* 1.3 79.8 - - - +
5B GLU* 1.3 68.0 + - + +
7B VAL* 3.9 0.7 - - - +
8B LYS* 3.0 48.9 + - + +
24B ASN* 3.0 26.4 + - - +
69B ILE* 4.1 25.2 - - + +
73B ASN* 5.5 0.2 - - - +
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Residues in contact with GLU 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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48A GLU* 3.8 0.8 - - - +
1B SER* 3.0 13.8 - - - -
2B THR* 2.9 43.9 + - + +
4B GLU* 1.3 82.8 - - + +
6B ARG* 1.3 59.0 + - - +
8B LYS* 3.9 4.5 - - - +
9B LYS* 3.0 29.8 + - - +
19B GLN* 4.5 3.0 + - - +
407B ZN 2.3 35.8 - - - -
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Residues in contact with ARG 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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1A SER* 5.0 0.8 + - - -
6A ARG* 3.7 36.3 - - - +
49A GLU* 3.9 11.2 + - - +
1B SER* 3.5 27.5 + - - +
2B THR 2.9 22.5 + - - +
3B ILE* 3.2 18.3 + - - +
5B GLU* 1.3 72.2 - - - +
7B VAL* 1.3 65.2 + - - +
9B LYS* 3.4 8.3 + - - +
10B ILE* 3.1 28.6 + - + +
49B GLU* 2.7 41.8 + - + +
50B PHE* 4.1 22.2 - - + -
76B GLN* 4.7 5.5 + - - -
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Residues in contact with VAL 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 ILE* 2.9 32.3 + - + +
4B GLU 3.9 2.7 - - - +
6B ARG* 1.3 72.8 - - - +
8B LYS* 1.3 68.2 + - - +
10B ILE* 3.1 4.0 + - - +
11B ILE* 2.9 43.0 + - + +
46B LEU* 4.4 14.6 - - + -
50B PHE* 3.8 24.0 - - + -
68B ALA* 4.5 10.8 - - + -
69B ILE* 3.9 24.2 - - + +
72B ILE* 4.3 14.1 - - + -
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Residues in contact with LYS 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 GLU* 3.0 37.8 + - + +
5B GLU* 3.9 4.7 - - - +
7B VAL* 1.3 77.0 - - - +
9B LYS* 1.3 57.4 + - - +
11B ILE* 3.4 4.2 + - - +
12B GLY 2.9 24.6 + - - -
19B GLN* 3.0 22.3 - - - +
22B VAL* 3.2 41.7 + - + +
23B THR* 4.3 1.6 - - - +
24B ASN* 2.7 41.0 + - - +
65B VAL* 4.1 14.4 - - + -
69B ILE* 4.4 1.8 - - + -
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Residues in contact with LYS 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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9A LYS* 6.3 1.8 - - + -
10A ILE* 4.9 13.9 - - - +
49A GLU* 3.6 23.7 + - - +
5B GLU 3.0 18.8 + - - +
6B ARG* 3.6 8.5 - - - +
7B VAL 3.2 0.2 - - - -
8B LYS* 1.3 77.2 - - - +
10B ILE* 1.3 57.8 + - + +
12B GLY* 3.3 1.2 + - - -
13B GLU* 2.9 57.9 + - + +
19B GLN* 3.6 17.4 - - + +
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Residues in contact with ILE 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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9A LYS* 5.5 6.3 - - - +
6B ARG* 3.1 18.1 + - + +
7B VAL 3.1 6.3 + - - +
9B LYS* 1.3 76.3 - - + +
11B ILE* 1.3 59.8 - - - +
13B GLU* 3.3 15.0 + - + +
14B GLN* 2.8 30.6 + - + +
42B LEU* 4.3 5.2 - - + -
45B ALA* 3.9 29.6 - - + +
46B LEU* 4.0 15.3 - - + -
49B GLU* 3.3 46.2 - - + +
50B PHE* 4.0 9.2 - - + -
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Residues in contact with ILE 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 VAL* 2.9 40.9 + - + +
8B LYS* 3.7 5.6 - - - +
10B ILE* 1.3 75.3 - - - +
12B GLY* 1.3 63.3 + - - +
14B GLN* 3.8 0.3 - - - +
15B LEU* 3.0 33.6 + - + +
17B VAL* 4.9 0.2 - - + -
22B VAL* 4.0 7.4 - - + -
28B PHE* 3.6 32.5 - - + -
32B LEU* 3.7 30.1 - - + -
42B LEU* 4.0 19.3 - - + -
46B LEU* 5.1 4.5 - - + -
65B VAL* 4.1 19.1 - - + -
68B ALA* 4.7 1.8 - - + -
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Residues in contact with GLY 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 LYS 2.9 14.7 + - - -
9B LYS 3.7 2.9 - - - -
10B ILE 3.2 0.2 - - - -
11B ILE* 1.3 78.1 - - - +
13B GLU* 1.3 57.1 + - - +
16B GLY* 2.9 26.2 + - - -
17B VAL* 3.1 34.9 + - - +
19B GLN* 4.0 7.9 - - - -
22B VAL* 4.2 1.1 - - - -
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Residues in contact with GLU 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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9A LYS* 4.4 24.1 + - - +
13A GLU* 4.6 13.9 - - - +
9B LYS* 2.9 48.0 + - + +
10B ILE* 3.9 17.5 - - + +
12B GLY* 1.3 77.5 - - - +
14B GLN* 1.3 64.6 + - - +
16B GLY* 3.4 7.8 + - - -
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Residues in contact with GLN 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 ILE* 2.8 22.9 + - - +
11B ILE 3.8 2.7 - - - +
13B GLU* 1.3 78.4 - - - +
15B LEU* 1.3 63.0 + - + +
16B GLY 3.7 0.3 + - - -
38B ASP* 4.8 5.8 - - - +
41B GLU* 3.4 38.9 + - - +
42B LEU* 3.5 39.3 - - + +
45B ALA* 3.7 15.1 - - + +
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Residues in contact with LEU 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 ILE* 3.0 24.3 + - + +
14B GLN* 1.3 83.0 - - + +
16B GLY* 1.3 64.6 + - - +
17B VAL* 3.4 17.6 + - + +
28B PHE* 4.3 9.6 - - + -
32B LEU* 3.6 43.8 - - + +
33B GLY 6.0 0.2 - - - -
34B ALA* 3.8 20.4 - - + -
38B ASP* 3.6 38.8 - - + +
42B LEU* 4.7 7.9 - - + -
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Residues in contact with GLY 16 (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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12B GLY 2.9 10.1 + - - -
13B GLU* 3.4 6.7 + - - -
14B GLN 3.4 4.0 + - - -
15B LEU* 1.3 78.8 - - - +
17B VAL* 1.3 59.4 + - - +
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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