Contacts of the strand formed by residues 92 - 103 (chain A) in PDB entry 1EQR
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 ILE 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 24.0 - - + +
10A ARG* 3.9 8.7 - - - +
11A LEU* 3.4 31.4 - - + +
14A VAL* 3.8 11.9 - - + -
45A VAL* 3.5 29.4 - - + -
46A GLN* 4.6 1.6 + - - +
75A VAL* 4.0 9.6 - - + -
76A ARG 3.2 15.9 - - - +
78A ARG* 2.6 29.2 + - - +
89A THR* 3.3 24.7 - - - +
91A GLU* 1.3 85.1 - - - +
93A GLU* 1.3 66.0 - - - +
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Residues in contact with GLU 93 (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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35A PHE* 4.2 7.3 - - - -
46A GLN* 3.2 42.9 + - + +
48A PHE* 4.2 11.4 - - + -
74A THR 3.8 0.2 - - - +
75A VAL* 3.6 2.8 - - - -
76A ARG* 2.5 80.4 + - + +
77A ALA 4.9 1.0 - - - +
78A ARG* 3.8 16.1 - - + +
92A ILE* 1.3 81.9 - - - +
94A VAL* 1.3 69.7 + - - +
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Residues in contact with VAL 94 (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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9A LEU* 3.9 19.7 - - + -
18A VAL* 4.2 6.5 - - + -
20A LEU* 4.2 7.4 - - + -
45A VAL* 4.2 8.1 - - + -
46A GLN 2.9 12.9 + - - +
47A VAL* 3.4 9.4 - - + +
48A PHE 2.7 29.5 + - - -
71A VAL* 4.6 12.1 - - + -
73A GLY* 3.7 31.6 - - - +
74A THR 3.3 8.1 - - - +
75A VAL* 3.8 21.8 - - + -
92A ILE* 5.0 0.2 - - + -
93A GLU* 1.3 79.6 - - - +
95A LEU* 1.3 56.3 + - - +
96A ALA 3.1 5.7 + - - +
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Residues in contact with LEU 95 (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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48A PHE* 3.5 30.3 - - + +
50A ASP* 3.5 34.3 - - + +
53A ARG* 3.7 22.5 + - - +
73A GLY* 3.4 0.3 - - - -
74A THR* 2.8 44.3 + - - +
76A ARG* 3.9 31.6 - - - +
93A GLU* 4.0 3.2 + - - +
94A VAL* 1.3 67.4 - - - +
96A ALA* 1.3 65.2 + - - +
97A SER* 4.8 1.2 - - - -
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Residues in contact with ALA 96 (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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47A VAL* 3.8 19.5 - - + -
48A PHE 2.8 18.0 + - - +
49A PHE* 3.9 24.2 - - + -
50A ASP* 3.2 20.7 - - - +
53A ARG* 3.8 5.4 - - - -
56A ALA* 5.4 2.0 - - + -
71A VAL* 4.5 3.4 - - + -
72A THR 4.0 2.2 - - - +
73A GLY* 3.9 9.4 - - - -
94A VAL* 3.1 4.7 + - - -
95A LEU* 1.3 76.6 - - - +
97A SER* 1.3 60.2 + - - +
98A SER 4.4 8.1 - - - +
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Residues in contact with SER 97 (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 GLN* 5.1 7.7 + - - +
53A ARG* 3.4 42.1 - - - +
56A ALA* 4.1 10.8 - - - +
72A THR* 3.1 20.8 + - - +
73A GLY* 4.4 4.7 - - - -
74A THR* 5.9 1.3 - - - -
95A LEU 4.8 0.2 - - - -
96A ALA* 1.3 73.7 - - - +
98A SER* 1.3 67.7 + - - +
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Residues in contact with SER 98 (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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56A ALA* 4.0 8.1 - - - +
70A GLN* 5.6 0.7 + - - -
71A VAL* 3.2 9.7 - - - +
72A THR* 3.2 50.2 + - - +
96A ALA* 3.7 2.5 - - - +
97A SER* 1.3 87.2 + - - +
99A LEU* 1.3 67.3 + - - +
100A THR* 5.3 1.7 + - - -
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Residues in contact with LEU 99 (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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49A PHE* 3.7 23.3 - - + -
56A ALA* 3.7 14.9 - - + +
59A LEU* 3.7 25.2 - - + +
60A ALA* 3.5 38.1 - - + +
63A LEU* 3.8 11.4 - - + -
69A ILE* 3.9 27.4 - - + -
70A GLN 3.4 16.6 - - - +
71A VAL* 4.0 13.0 - - + -
98A SER* 1.3 78.6 + - - +
100A THR* 1.3 70.1 + - - +
101A ILE* 4.2 2.7 - - + +
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Residues in contact with THR 100 (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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59A LEU* 4.8 2.6 - - - +
69A ILE* 3.3 2.1 - - - -
70A GLN* 2.8 49.8 + - + +
98A SER* 5.3 2.0 + - - -
99A LEU* 1.3 80.5 + - - +
101A ILE* 1.3 69.6 + - - +
102A ILE* 3.2 16.5 + - + +
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Residues in contact with ILE 101 (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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59A LEU* 3.9 35.3 - - + +
62A GLU* 4.1 16.8 - - + +
63A LEU* 3.6 30.3 - - + -
67A PHE* 3.8 30.3 - - + -
68A CYS 3.8 4.7 - - - +
69A ILE* 4.2 2.7 - - + -
99A LEU* 4.7 2.2 - - + -
100A THR* 1.3 76.0 - - - +
102A ILE* 1.3 62.3 + - - +
103A ASN* 4.0 16.2 - - - +
104A ARG* 4.4 9.9 - - + +
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Residues in contact with ILE 102 (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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21A CYS* 5.2 0.7 - - - -
68A CYS* 2.6 21.5 + - + +
69A ILE 4.4 8.1 - - - +
70A GLN* 4.4 14.1 - - + +
100A THR* 3.2 20.1 + - + +
101A ILE* 1.3 75.1 - - - +
103A ASN* 1.3 69.0 + - + +
238B PHE* 3.8 30.3 - - + -
491B HIS* 4.1 15.0 + - + +
525B THR 4.3 7.4 - - - +
527B PRO* 3.7 31.6 - - + -
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Residues in contact with ASN 103 (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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67A PHE* 3.5 2.4 - - - +
68A CYS* 2.7 36.4 + - + +
101A ILE* 3.4 5.7 - - - -
102A ILE* 1.3 87.6 + - - +
104A ARG* 1.3 71.0 + - - +
491B HIS* 3.2 17.3 + - - +
492B ASN* 5.2 6.1 - - - +
524B GLY* 3.9 1.1 - - - -
525B THR* 2.7 55.4 - - - +
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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