Contacts of the helix formed by residues 4 - 21 (chain A) in PDB entry 3LRA
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 3.2 14.1 + - + +
3A VAL* 1.3 74.4 - - - +
5A LYS* 1.3 66.8 + - - +
6A GLN* 2.7 40.4 - - + +
7A ASP* 2.6 59.9 + - - +
8A THR* 3.3 15.3 + - - +
50A ILE* 4.6 0.2 - - - -
54A GLU* 3.4 17.5 - - - +
106A MET* 5.7 0.8 - - - +
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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
----------------------------------------------------------
3A VAL 3.9 0.2 + - - -
4A ARG* 1.3 71.2 - - - +
6A GLN* 1.3 63.2 + - - +
8A THR* 2.8 26.4 + - - +
9A GLN* 2.8 36.3 - - + +
47A GLN* 3.2 39.1 + - - +
50A ILE* 4.1 16.7 - - + +
51A ASP* 2.6 32.0 + - - -
54A GLU* 2.9 18.5 + - - +
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Residues in contact with GLN 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 2.7 47.2 - - + +
5A LYS* 1.3 79.6 - - - +
7A ASP* 1.3 59.0 + - - +
9A GLN* 3.1 9.4 + - - +
10A ARG* 2.6 39.1 + - + +
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Residues in contact with ASP 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.8 1.7 - - + -
4A ARG* 2.6 66.7 + - - +
6A GLN* 1.3 83.2 - - - +
8A THR* 1.3 55.0 + - - +
9A GLN 2.9 0.2 + - - -
10A ARG* 3.0 2.8 + - - -
11A ALA* 2.7 38.5 + - - +
102A PHE* 3.7 19.9 - - + -
106A MET* 3.5 32.8 - - - +
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.3 31.4 - - + -
4A ARG 3.4 8.7 - - - +
5A LYS* 2.8 15.6 + - - +
7A ASP* 1.3 74.6 - - - +
9A GLN* 1.3 64.5 + - - +
11A ALA* 4.3 1.8 - - - -
12A LEU* 3.0 27.7 + - - +
41A PHE* 3.4 30.9 - - + -
46A PHE* 4.9 1.6 - - + -
50A ILE* 3.7 32.9 - - + +
106A MET* 4.8 1.8 - - - -
112A LEU* 5.0 2.7 - - + -
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Residues in contact with GLN 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 45.9 + - + +
6A GLN* 3.1 10.8 - - - +
7A ASP 2.9 0.2 - - - -
8A THR* 1.3 84.8 + - - +
10A ARG* 1.3 60.4 + - - +
11A ALA 3.1 0.7 - - - -
12A LEU* 2.9 10.5 + - - +
13A HIS* 2.9 27.8 + - - +
47A GLN* 5.6 4.9 - - - +
50A ILE* 6.1 0.4 - - - +
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 2.6 20.7 + - + +
7A ASP* 3.8 4.2 + - - +
9A GLN* 1.3 72.6 - - - +
11A ALA* 1.3 57.5 + - - +
13A HIS* 3.4 7.0 + - + +
14A LEU* 3.0 52.8 + - + +
98A GLU* 3.4 37.8 + - - +
99A ASP* 3.4 22.8 + - - +
102A PHE* 3.6 37.2 - - + +
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Residues in contact with ALA 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 ASP 2.7 21.9 + - - +
8A THR* 3.9 7.2 - - - +
10A ARG* 1.3 71.0 - - - +
12A LEU* 1.3 59.5 + - - +
14A LEU* 4.6 3.4 - - - -
15A LEU* 2.9 34.3 + - - +
41A PHE* 4.5 4.0 - - + -
102A PHE* 3.7 21.0 - - + -
103A LEU* 5.3 2.5 - - + +
106A MET* 4.4 4.7 - - + -
107A PHE* 4.3 26.1 - - + -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR 3.0 18.5 + - - +
9A GLN* 2.9 12.4 + - - +
11A ALA* 1.3 76.1 - - - +
13A HIS* 1.3 67.8 + - - +
15A LEU* 4.0 2.8 - - + +
16A GLU* 3.0 63.4 + - - +
37A VAL 5.1 0.2 - - - -
38A ILE* 3.7 30.1 - - + +
41A PHE* 3.3 34.5 - - + -
42A GLN* 4.4 13.0 - - + +
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Residues in contact with HIS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN 2.9 11.5 + - - +
10A ARG* 3.5 12.3 - - + +
11A ALA 3.3 0.2 - - - -
12A LEU* 1.3 79.4 - - - +
14A LEU* 1.3 78.2 + - + +
16A GLU* 3.1 10.2 + - - +
17A GLU* 3.0 46.3 + - + +
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Residues in contact with LEU 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 ARG* 3.0 37.6 + - + +
11A ALA* 4.2 2.5 - - - +
13A HIS* 1.3 96.2 + - + +
15A LEU* 1.3 63.9 + - - +
17A GLU* 3.0 21.4 + - - +
18A TYR* 3.1 33.1 + - + -
99A ASP* 4.1 35.2 - - + +
102A PHE* 3.7 31.2 - - + -
103A LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 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 ALA 2.9 20.6 + - - +
12A LEU* 4.0 3.8 - - + +
14A LEU* 1.3 76.8 - - - +
16A GLU* 1.3 61.3 + - - +
18A TYR* 3.9 4.3 + - - +
19A ARG* 3.5 9.4 + - - +
34A ILE* 3.3 46.1 - - + +
37A VAL* 3.3 41.1 - - + -
38A ILE* 3.8 11.0 - - + +
41A PHE* 5.5 1.3 - - + -
86A LEU* 4.5 8.7 - - + -
90A LEU* 3.6 29.4 - - + -
103A LEU* 5.6 4.7 - - + +
107A PHE* 4.3 18.4 - - + -
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.0 43.8 + - - +
13A HIS* 3.1 9.0 + - - +
15A LEU* 1.3 73.0 - - - +
17A GLU* 1.3 70.3 + - - +
19A ARG* 3.0 21.7 + - - +
20A SER* 3.4 7.1 + - - -
38A ILE* 3.3 30.0 - - + +
42A GLN* 3.4 17.8 + - - -
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Residues in contact with GLU 17 (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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13A HIS* 3.0 39.5 + - + +
14A LEU* 3.2 16.8 - - - +
16A GLU* 1.3 76.9 - - - +
18A TYR* 1.3 83.7 + - - +
19A ARG 3.0 2.4 + - - -
20A SER* 2.6 28.6 + - - +
21A LYS* 3.7 25.0 + - - +
99A ASP* 5.3 0.5 - - - +
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Residues in contact with TYR 18 (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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14A LEU* 3.1 37.7 + - + +
15A LEU* 4.2 6.1 - - - +
17A GLU* 1.3 98.2 + - - +
19A ARG* 1.3 59.6 + - - +
20A SER 3.4 0.2 - - - -
21A LYS* 4.0 26.5 + - + +
22A LEU* 3.6 21.5 - - - +
34A ILE* 4.6 2.5 - - - +
90A LEU* 4.1 22.1 - - + +
93A HIS* 4.2 29.7 - - + +
94A VAL* 3.8 30.3 - - + +
95A ASP 4.7 3.4 + - - -
96A SER* 4.7 1.6 - - - -
99A ASP* 2.8 27.8 + - + -
103A LEU* 4.7 12.3 - - + -
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Residues in contact with ARG 19 (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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15A LEU 3.5 13.3 + - - +
16A GLU* 3.0 15.5 + - - +
17A GLU 3.0 0.4 + - - -
18A TYR* 1.3 78.6 - - - +
20A SER* 1.3 62.2 + - - +
22A LEU* 3.6 7.9 - - - +
31A ARG* 2.6 97.8 + - + +
32A SER* 5.0 1.8 - - - +
34A ILE* 3.9 19.7 - - + -
35A GLU* 3.6 31.7 + - - +
38A ILE* 4.9 9.9 - - - -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU 3.4 5.5 + - - -
17A GLU* 2.6 23.5 + - - +
19A ARG* 1.3 76.4 - - - +
21A LYS* 1.3 57.3 + - - +
22A LEU 2.8 26.1 + - - +
31A ARG* 4.3 7.7 + - - +
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Residues in contact with LYS 21 (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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17A GLU* 3.7 30.1 + - - +
18A TYR* 4.0 26.1 + - + +
19A ARG 3.5 1.0 - - - -
20A SER* 1.3 85.4 + - - +
22A LEU* 1.3 67.3 + - - +
93A HIS* 5.3 5.3 + - + +
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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