Contacts of the strand formed by residues 3 - 12 (chain A) in PDB entry 1LEG
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 HIS 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY* 3.2 32.6 + - - -
2A PRO* 1.3 77.0 + - - +
4A SER* 1.3 62.5 + - - +
29A ASP* 2.6 30.7 + - - +
102A GLU* 3.3 6.4 - - - +
103A VAL* 2.9 33.4 + - + -
104A GLY 5.1 4.9 - - - -
105A SER* 5.5 1.1 - - - -
168A LEU* 3.7 5.7 - - + +
172A LEU* 3.6 37.5 - - + +
179A LEU 4.4 5.4 - - - -
180A LEU* 3.7 28.7 - - + +
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Residues in contact with SER 4 (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 HIS* 1.3 76.9 - - - +
5A LEU* 1.3 60.5 + - - +
6A ARG* 3.5 28.7 + - - +
27A TYR 3.7 0.2 - - - +
28A VAL* 3.2 7.4 - - - -
29A ASP* 2.9 36.8 + - - +
101A CYS 3.3 11.9 - - - -
102A GLU* 4.3 11.2 - - - -
113A TYR* 4.4 4.3 - - - -
168A LEU* 3.6 8.3 - - - +
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Residues in contact with LEU 5 (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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4A SER* 1.3 72.9 - - - +
6A ARG* 1.3 62.2 + - - +
7A TYR* 3.8 24.5 - - + -
27A TYR 3.4 14.8 - - - +
28A VAL* 4.3 4.0 - - + -
33A PHE* 3.7 28.0 - - + -
100A GLY* 3.0 5.2 - - - -
101A CYS* 2.9 36.3 + - - +
113A TYR* 3.7 1.0 + - - -
164A CYS* 3.7 33.9 - - - +
167A TRP* 4.7 0.2 - - + -
168A LEU* 3.8 21.5 - - + +
171A TYR* 4.2 17.7 - - + -
1P GLU 4.2 7.9 - - - +
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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
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4A SER* 3.5 20.2 + - - +
5A LEU* 1.3 78.7 - - - +
7A TYR* 1.3 64.7 + - - +
8A PHE* 4.2 24.0 - - + -
25A VAL 3.9 0.9 - - - +
26A GLY* 3.3 2.6 - - - -
27A TYR* 2.7 61.0 + - + +
29A ASP* 2.4 36.3 + - - +
30A ASP* 4.6 8.5 + - - +
98A ILE* 4.1 15.3 - - + -
99A SER 3.4 4.7 - - - -
113A TYR* 3.6 20.0 - - - +
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Residues in contact with TYR 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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5A LEU* 3.8 23.7 - - + +
6A ARG* 1.3 76.8 - - - +
8A PHE* 1.3 62.1 + - - +
9A VAL* 4.0 3.7 - - + +
24A GLU* 4.7 0.2 - - - -
25A VAL 3.4 4.0 - - - -
26A GLY* 3.7 21.5 - - - -
33A PHE* 3.6 13.9 - + - -
34A VAL* 3.9 8.0 - - + +
45A TYR* 3.6 22.0 - + - -
59A TYR* 4.5 1.6 + - - -
63A GLU* 4.6 0.9 + - - -
97A VAL 3.6 1.4 - - - +
98A ILE* 3.4 7.4 - - - +
99A SER* 2.8 41.2 + - - +
100A GLY* 5.4 0.4 - - - -
159A TYR* 3.9 7.9 - - - -
171A TYR* 4.2 0.7 + - - -
1P GLU* 3.1 49.1 + - - -
2P GLN* 3.4 39.4 + - + +
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Residues in contact with PHE 8 (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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6A ARG* 4.2 32.8 - - + -
7A TYR* 1.3 74.6 - - - +
9A VAL* 1.3 61.7 + - - +
10A THR* 5.0 0.3 + - - -
23A MET 3.9 0.9 - - - +
24A GLU* 3.5 2.9 - - - -
25A VAL* 2.8 34.7 + - + +
27A TYR* 3.6 37.5 - + - -
97A VAL 3.5 3.4 - - - -
98A ILE* 4.0 19.7 - - + -
54B MET* 4.7 7.1 - - - +
55B SER* 4.0 14.8 - - - -
56B PHE* 3.5 65.7 - + + -
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Residues in contact with VAL 9 (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 TYR* 4.8 2.7 - - + -
8A PHE* 1.3 76.9 - - - +
10A THR* 1.3 69.2 + - - +
22A TYR* 3.3 35.0 - - + +
23A MET 3.4 2.7 - - - +
24A GLU* 3.8 10.3 - - + -
74A PHE* 3.9 19.5 - - + -
95A ILE 5.7 0.4 - - - +
96A GLN* 3.3 4.9 - - - -
97A VAL* 2.9 42.8 + - + +
99A SER* 6.2 0.4 - - - -
56B PHE* 3.3 3.2 - - - -
2P GLN* 3.6 24.0 - - - +
5P PHE* 4.3 15.7 - - + -
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Residues in contact with THR 10 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE 5.0 0.3 - - - -
9A VAL* 1.3 78.3 - - - +
11A ALA* 1.3 63.3 + - - +
12A VAL* 3.7 12.6 - - + -
21A ARG 3.7 1.1 - - - +
22A TYR* 3.4 7.2 - - - -
23A MET* 2.9 39.3 + - - +
94A THR* 3.6 22.0 - - + -
95A ILE 3.3 11.0 - - - +
96A GLN* 4.0 1.8 - - + -
33B PRO* 5.0 0.4 - - + -
54B MET* 3.6 15.8 - - + +
56B PHE* 3.3 20.3 - - - -
62B PHE* 3.6 16.6 - - + -
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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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10A THR* 1.3 73.6 - - - +
12A VAL* 1.3 63.5 + - - +
13A SER 4.2 0.2 - - - -
20A PRO* 5.2 1.6 - - + -
21A ARG 3.3 5.8 - - - +
22A TYR* 4.1 6.5 - - + -
74A PHE* 3.7 32.5 - - + -
78A LEU* 4.0 18.6 - - + +
93A HIS 3.8 0.7 - - - +
94A THR* 3.4 4.2 - - - -
95A ILE* 2.9 40.6 + - + +
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Residues in contact with VAL 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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10A THR* 3.7 9.6 - - + -
11A ALA* 1.3 80.2 - - - +
13A SER* 1.3 63.8 + - - +
14A ARG* 4.4 2.6 - - + +
20A PRO* 3.2 4.6 - - - +
21A ARG* 2.9 45.0 + - + +
92A SER* 3.6 20.4 - - - +
93A HIS 3.4 6.3 - - - +
94A THR* 3.6 11.2 - - + +
32B PRO* 6.3 0.2 - - + -
33B PRO* 3.4 37.5 - - + -
34B HIS* 5.4 7.2 - - + +
990B PO4 6.0 0.4 - - - +
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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