Contacts of the helix formed by residues 3 - 17 (chain A) in PDB entry 1FXT
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 ARG 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 71.4 + - - +
4A ALA* 1.3 60.7 + - - +
6A ARG* 3.6 2.5 + - - +
7A ILE* 3.5 19.6 + - - +
32A ILE* 3.7 28.6 - - + +
33A HIS* 3.4 39.1 + - - +
57A GLU* 2.9 34.1 + - - -
58A VAL* 2.7 39.6 + - + -
59A PRO 3.5 11.1 - - - -
60A MET* 3.6 38.6 + - - +
62A TYR* 3.1 23.4 + - + +
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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
----------------------------------------------------------
2A SER* 3.5 8.4 + - - +
3A ARG* 1.3 77.0 - - - +
5A LYS* 1.3 56.5 + - - +
6A ARG 3.2 5.4 + - - -
8A MET* 4.1 24.4 + - - +
32A ILE* 4.0 31.0 - - + +
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Residues in contact with LYS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.3 23.1 + - - +
4A ALA* 1.3 73.9 - - - +
6A ARG* 1.3 58.2 + - - +
9A LYS* 2.8 54.3 + - - +
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Residues in contact with ARG 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 3.6 11.4 - - - +
3A ARG 3.8 5.2 - - - +
4A ALA 3.2 3.4 + - - -
5A LYS* 1.3 78.4 - - - +
7A ILE* 1.4 65.3 - - - +
8A MET 3.5 1.3 - - - +
9A LYS* 3.4 24.6 + - - +
10A GLU* 2.8 52.0 + - - +
62A TYR* 3.1 38.6 + - + +
63A PRO* 3.6 38.7 + - + +
96A TRP* 3.9 2.0 - - - +
98A PRO 2.8 26.0 + - - -
99A VAL* 4.1 3.1 - - - +
100A ILE 2.9 35.7 + - - +
101A THR* 3.7 4.8 - - - +
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Residues in contact with ILE 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 ARG* 3.5 5.4 + - + +
6A ARG* 1.4 76.3 - - - +
8A MET* 1.3 58.9 + - - +
10A GLU* 3.1 16.9 + - + +
11A ILE* 2.9 46.2 + - + +
26A PHE* 4.3 3.6 - - + -
32A ILE* 3.5 41.1 - - + +
33A HIS* 4.2 0.7 - - - +
35A LEU* 4.0 10.1 - - + -
58A VAL* 3.8 18.6 - - + -
62A TYR* 3.6 24.9 - - + -
102A LEU* 3.7 28.3 - - + -
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Residues in contact with MET 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA 4.1 12.3 + - - +
6A ARG 3.5 1.2 + - - +
7A ILE* 1.3 73.3 - - - +
9A LYS* 1.3 57.1 + - + +
11A ILE* 4.1 28.6 - - + +
12A GLN* 3.3 27.7 + - - +
26A PHE* 4.8 2.5 - - + -
30A SER* 5.0 10.8 - - - +
31A ASP 3.9 21.3 - - - +
32A ILE* 4.0 18.1 - - + +
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 2.8 64.8 + - - +
6A ARG* 3.4 14.6 + - - +
7A ILE 3.3 0.6 - - - -
8A MET* 1.3 74.5 - - - +
10A GLU* 1.3 58.1 + - + +
12A GLN* 4.1 2.4 - - - +
13A ALA* 3.0 32.7 + - - +
101A THR* 6.3 0.4 - - + -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 2.8 48.0 + - - +
7A ILE* 3.1 18.1 + - + +
9A LYS* 1.3 73.4 - - + +
11A ILE* 1.3 58.4 + - - +
13A ALA* 4.6 3.8 - - - -
14A VAL* 3.1 36.7 + - - +
24A LEU* 3.8 16.6 - - + -
62A TYR* 2.7 25.7 + - - -
101A THR* 3.8 19.3 - - + +
102A LEU* 2.9 30.5 + - - +
103A LYS* 4.7 4.3 - - + +
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 2.9 37.7 + - + +
8A MET* 4.2 21.5 - - + +
10A GLU* 1.3 72.2 - - - +
12A GLN* 1.3 57.1 + - - +
14A VAL* 3.9 2.5 - - - +
15A LYS* 3.0 33.7 + - + +
24A LEU* 3.7 36.1 - - + +
26A PHE* 3.7 33.0 - - + -
35A LEU* 3.8 9.6 - - + -
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Residues in contact with GLN 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 MET 3.3 17.4 + - - +
9A LYS* 4.3 2.5 - - - +
10A GLU 3.6 0.2 - - - -
11A ILE* 1.3 77.3 - - - +
13A ALA* 1.3 57.3 + - - +
15A LYS* 3.2 41.5 + - - +
16A ASP* 2.9 67.8 + - - +
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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
----------------------------------------------------------
9A LYS 3.0 23.8 + - - +
10A GLU* 4.2 4.7 - - - +
12A GLN* 1.3 71.7 - - - +
14A VAL* 1.3 56.1 + - - +
16A ASP* 4.2 6.3 + - - +
17A ASP* 3.6 9.7 + - - +
103A LYS* 2.8 40.7 + - + +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.1 21.8 + - - +
11A ILE* 4.0 2.7 - - - +
13A ALA* 1.3 72.2 - - - +
15A LYS* 1.3 65.9 + - - +
17A ASP 3.4 20.1 + - - +
18A PRO* 5.1 0.3 - - - +
20A ALA* 6.2 0.7 - - + -
22A ILE* 3.1 42.5 - - + +
23A THR* 4.4 0.7 - - - -
24A LEU* 3.8 33.2 - - + +
103A LYS* 3.8 33.2 - - + +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.0 23.7 + - + +
12A GLN* 3.2 36.6 + - - +
14A VAL* 1.3 76.0 - - - +
16A ASP* 1.3 60.6 + - - +
17A ASP 3.6 0.5 + - - -
18A PRO* 4.5 7.1 - - - +
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 2.9 51.4 + - - +
13A ALA* 4.4 6.5 + - - +
14A VAL 3.5 0.2 - - - -
15A LYS* 1.3 71.2 - - - +
17A ASP* 1.3 58.3 + - + +
18A PRO* 3.5 9.0 - - - +
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.6 3.5 + - - +
14A VAL* 3.4 18.3 + - - +
16A ASP* 1.3 78.8 - - + +
18A PRO* 1.4 59.6 - - - +
19A ALA* 3.4 13.3 + - - +
20A ALA* 3.1 29.5 + - - +
21A HIS 4.6 1.0 + - - -
22A ILE 5.5 2.9 + - - +
103A LYS* 2.7 38.9 + - - +
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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