Contacts of the helix formed by residues 6 - 18 (chain B) in PDB entry 4NFT
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 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU* 3.7 19.4 + - + -
5B SER* 1.3 75.6 - - - +
7B SER* 1.3 59.5 + - - +
8B ILE 3.4 2.5 - - - -
9B TYR* 2.9 14.9 + + + +
10B VAL* 2.9 32.3 + - + +
32B ASN* 2.7 12.7 + - - +
35B VAL* 3.5 33.7 - - + -
36B ASN* 4.0 20.4 - - - -
39B PHE* 4.7 3.6 - + - -
107B PHE* 4.5 10.5 - + + -
108B PRO* 4.2 24.5 - - + -
111B ARG* 3.5 22.2 + - + -
112B ILE* 3.9 24.4 - - + +
115B HIS* 3.0 30.5 + + - +
138B LEU* 5.5 2.2 - - + -
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Residues in contact with SER 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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5B SER* 3.3 17.3 + - - -
6B TYR* 1.3 77.5 - - - +
8B ILE* 1.3 67.8 + - - +
10B VAL* 3.1 2.3 + - - -
11B TYR* 3.1 33.7 + - - -
28B MET* 3.3 35.5 - - - +
32B ASN* 3.5 13.7 + - - +
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Residues in contact with ILE 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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5B SER* 5.3 4.3 - - - +
6B TYR 3.4 0.8 - - - -
7B SER* 1.3 84.1 - - - +
9B TYR* 1.3 78.8 + - + +
11B TYR* 3.3 18.3 - - + +
12B LYS* 3.2 40.9 + - + +
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Residues in contact with TYR 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER 4.9 0.2 - - - -
6B TYR* 2.9 22.2 + + - +
8B ILE* 1.3 91.6 - - + +
10B VAL* 1.3 64.0 + - - +
12B LYS* 3.3 33.0 + - + +
13B VAL* 3.1 27.2 + - - +
106B GLN* 3.5 19.3 - - - +
107B PHE* 4.1 17.4 - - + -
108B PRO* 3.5 47.3 - - + +
111B ARG* 3.6 23.7 + - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 2.9 24.8 + - + +
7B SER* 3.1 7.4 + - - +
9B TYR* 1.3 75.9 - - - +
11B TYR* 1.3 57.3 + - - +
13B VAL* 3.3 3.5 + - - +
14B LEU* 2.9 27.1 + - + +
23B ILE* 4.9 1.8 - - + -
28B MET* 3.7 27.4 - - + -
31B MET* 4.3 18.4 - - + +
32B ASN* 5.2 1.3 - - - +
35B VAL* 4.5 16.4 - - + -
107B PHE* 4.4 2.7 - - + -
142B THR* 4.2 21.3 - - + -
146B LEU* 3.6 23.2 - - + +
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Residues in contact with TYR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 3.1 31.6 + - - -
8B ILE* 3.3 18.4 - - + +
10B VAL* 1.3 74.9 - - - +
12B LYS* 1.3 65.0 + - - +
14B LEU* 3.2 10.1 + - + +
15B LYS* 3.0 39.8 + - - +
22B GLY* 6.3 0.2 - - - -
23B ILE* 3.5 35.7 + - + -
25B SER* 5.8 2.4 - - - -
28B MET* 3.4 24.8 - - + +
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.2 26.7 + - + +
9B TYR* 3.3 42.0 + - + +
11B TYR* 1.3 79.4 - - - +
13B VAL* 1.3 61.5 + - - +
15B LYS* 3.3 34.0 + - + +
16B GLN* 3.2 19.1 - - - +
106B GLN* 4.0 34.3 + - + +
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Residues in contact with VAL 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 TYR 3.1 14.6 + - - +
10B VAL 3.6 7.2 - - - +
12B LYS* 1.3 72.9 - - - +
14B LEU* 1.3 60.8 + - - +
15B LYS 3.1 1.8 - - - -
16B GLN* 2.9 28.2 + - + +
17B VAL* 3.2 12.7 + - + +
106B GLN* 4.0 9.6 - - + -
107B PHE* 3.9 13.5 - - + -
139B GLU* 3.7 27.8 - - + +
142B THR* 4.4 4.3 - - + -
143B ALA* 3.7 39.0 - - + +
146B LEU* 4.1 9.4 - - + -
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Residues in contact with LEU 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 VAL* 2.9 15.1 + - + +
11B TYR* 3.2 14.6 + - + +
13B VAL* 1.3 75.6 - - - +
15B LYS* 1.3 57.7 + - + +
17B VAL* 4.6 3.6 - - + +
18B HIS* 2.8 53.8 + - + +
21B THR* 3.5 23.6 - - - +
22B GLY* 4.1 6.1 - - - +
23B ILE* 3.9 34.1 - - + -
146B LEU* 3.8 23.1 - - + +
161B ILE* 4.1 22.0 - - + -
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Residues in contact with LYS 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 TYR* 3.0 36.7 + - - +
12B LYS* 3.5 25.7 - - - +
13B VAL 3.1 0.6 - - - -
14B LEU* 1.3 76.7 - - + +
16B GLN* 1.3 61.9 + - + +
18B HIS 4.9 0.2 - - - -
19B PRO* 3.4 32.9 - - + +
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Residues in contact with GLN 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 LYS 3.2 15.6 - - - +
13B VAL* 2.9 12.9 + - + +
15B LYS* 1.3 79.0 - - - +
17B VAL* 1.3 67.5 + - + +
19B PRO* 4.3 5.2 - - - +
106B GLN* 3.5 37.2 + - + +
139B GLU* 4.9 3.6 + - - -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.2 14.9 + - + +
14B LEU* 4.1 4.3 - - + +
16B GLN* 1.3 85.9 - - + +
18B HIS* 1.3 82.5 + - + +
19B PRO* 3.7 4.0 - - - +
143B ALA* 4.2 26.2 - - + +
146B LEU* 4.2 4.9 - - + -
147B GLU* 3.5 52.6 - - + +
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 2.8 25.7 + - + +
15B LYS* 4.9 0.2 - - - -
17B VAL* 1.3 96.8 + - + +
19B PRO* 1.3 68.4 - - + +
20B ASP* 3.2 7.9 - - - +
21B THR* 3.0 38.1 + - - +
146B LEU 3.6 3.0 + - - -
147B GLU* 3.1 41.2 + - - -
150B GLY* 3.3 16.1 - - - -
151B ASN* 3.2 30.2 + - - -
154B LYS* 6.1 1.2 - - + +
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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