Contacts of the strand formed by residues 4 - 15 (chain A) in PDB entry 4EJX
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 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLU* 3.7 26.1 + - + +
3A LYS* 1.3 80.5 - - - +
5A TYR* 1.3 63.7 + - - +
6A TYR* 3.3 31.5 + - - +
87A TYR* 3.3 45.0 - + + +
89A HIS* 3.2 24.3 + + - +
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Residues in contact with TYR 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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3A LYS* 3.4 32.6 - - + -
4A HIS* 1.3 77.4 - - - +
6A TYR* 1.3 62.8 - - - +
7A ILE* 3.8 18.4 - - + -
55A GLN* 3.1 32.3 - - - +
56A TYR 5.2 0.2 - - - -
76A PRO* 6.2 0.2 - - + -
77A ILE 4.0 13.5 + - - -
78A ILE* 4.2 17.7 - - + -
79A LYS* 3.6 21.1 + - - +
86A VAL* 3.9 29.2 - - + -
87A TYR 3.6 5.9 + - - +
88A VAL* 3.9 4.0 - - + -
89A HIS* 3.2 28.4 + - - -
189A GLU* 3.6 12.4 + - + -
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Residues in contact with TYR 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 HIS* 3.3 30.2 + - + +
5A TYR* 1.3 73.4 - - - +
7A ILE* 1.3 61.9 + - - +
55A GLN* 4.7 1.0 - - - +
56A TYR* 3.0 45.9 + - + +
57A THR* 3.2 21.7 + - - -
58A ASP* 3.6 14.4 - - - +
59A GLU* 3.5 41.9 + - + -
61A PHE* 3.1 24.2 - + + -
89A HIS* 3.2 36.5 + + + -
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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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5A TYR* 4.1 21.5 - - + -
6A TYR* 1.3 73.9 - - - +
8A GLY* 1.3 62.0 + - - +
53A TYR* 3.5 37.0 - - + -
54A LEU 3.4 6.7 - - - +
55A GLN* 4.6 2.0 - - + -
61A PHE* 3.4 4.4 - - - -
76A PRO* 3.6 26.2 - - + -
78A ILE* 4.1 17.9 - - + -
88A VAL* 3.6 26.7 - - + -
89A HIS 2.7 26.4 + - - +
90A LEU* 3.2 13.9 - - + -
91A LYS 2.9 15.7 + - - -
100A PHE* 5.0 2.5 - - + -
160A TYR* 4.6 4.7 - - + +
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Residues in contact with GLY 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 TYR 3.7 0.4 + - - -
7A ILE* 1.3 76.3 - - - +
9A ILE* 1.3 63.5 + - - -
10A ILE* 3.7 1.7 + - - -
52A LEU 3.4 2.1 - - - +
53A TYR* 4.7 0.9 - - - -
54A LEU* 2.8 44.2 + - - +
56A TYR* 3.7 20.9 + - - -
61A PHE* 4.6 2.5 - - - -
91A LYS* 3.4 10.8 - - - -
93A LEU* 5.5 2.0 - - - -
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Residues in contact with ILE 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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8A GLY* 1.3 70.5 - - - -
10A ILE* 1.3 73.7 + - - +
51A ALA* 4.4 0.9 - - + -
52A LEU 3.2 2.9 - - - -
53A TYR* 3.5 31.9 - - + -
90A LEU* 3.7 21.5 - - + -
91A LYS 2.9 10.5 + - - +
92A ASN* 3.7 13.0 - - - +
93A LEU* 3.2 24.8 + - - +
94A ALA* 3.4 8.7 + - + -
98A TYR* 3.5 50.0 - - + -
99A THR 4.1 3.8 - - - +
174A LEU* 3.6 22.9 - - + -
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Residues in contact with ILE 10 (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 GLY 3.7 1.1 + - - +
9A ILE* 1.3 80.2 - - - +
11A GLU* 1.3 66.5 + - - +
12A THR* 3.7 34.3 - - + -
51A ALA* 3.5 5.9 - - - -
52A LEU* 3.1 31.4 + - + +
54A LEU* 3.6 27.1 - - + -
56A TYR* 3.5 24.7 - - - +
93A LEU* 4.6 17.7 - - + -
94A ALA 4.8 2.9 - - - +
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Residues in contact with GLU 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 ILE* 1.3 81.5 - - - +
12A THR* 1.3 59.7 + - - +
49A LYS* 4.4 31.2 + - - +
50A LYS 3.6 7.6 - - - +
51A ALA* 4.7 0.2 - - - -
93A LEU 5.3 0.4 - - - +
94A ALA* 3.2 10.8 - - + +
95A SER* 2.7 42.2 + - - -
96A ARG 4.2 1.2 + - - -
212A TYR* 2.7 45.8 + - + +
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Residues in contact with THR 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 ILE* 3.7 25.4 - - + -
11A GLU* 1.3 75.1 - - - +
13A THR* 1.3 77.1 + - - +
14A TRP* 3.5 3.4 + - + -
49A LYS* 4.4 3.6 - - - -
50A LYS* 3.1 27.8 + - - +
52A LEU* 3.8 33.2 - - + +
54A LEU* 6.0 0.2 - - + -
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Residues in contact with THR 13 (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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12A THR* 1.3 83.1 + - - +
14A TRP* 1.3 61.4 + - - +
15A ASP 4.2 0.9 + - - -
47A LEU* 3.9 33.7 - - + +
48A TYR 3.8 4.7 - - - +
49A LYS* 4.3 10.0 - - - +
220A TYR* 3.7 25.4 + - + +
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Residues in contact with TRP 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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12A THR* 3.5 5.6 + - + +
13A THR* 1.3 75.2 - - - +
15A ASP* 1.3 83.8 + - + +
16A TYR* 4.0 27.2 - + - +
18A SER* 5.8 0.2 - - - -
46A ARG 3.5 2.4 - - - +
47A LEU* 3.2 6.6 - - - -
48A TYR* 2.9 43.9 + - - +
50A LYS* 4.4 12.3 - - + -
52A LEU* 4.8 17.7 - - + -
72A GLY* 3.7 18.2 - - - -
73A PHE* 4.0 25.8 - + + -
244A ASN 4.0 6.7 - - - -
245A GLY* 4.0 14.0 - - - -
246A TYR* 3.1 47.8 - + - -
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Residues in contact with ASP 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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13A THR 4.2 1.4 + - - -
14A TRP* 1.3 94.9 - - + +
16A TYR* 1.3 65.9 + - - +
17A ALA 3.5 0.9 - - - +
18A SER* 3.4 33.6 + - - +
46A ARG* 3.5 52.3 + - - +
47A LEU* 3.6 18.1 - - + +
246A TYR* 4.4 0.5 - - - -
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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