Contacts of the strand formed by residues 97 - 104 (chain A) in PDB entry 1EIC
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 TYR 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A SER 4.3 10.7 - - - +
26A CYS* 3.6 20.9 - - + +
27A ASN* 2.8 28.9 + - - +
30A MET* 3.5 45.4 - - + +
36A THR* 3.6 6.3 - - + +
40A CYS* 3.5 7.6 - - - +
41A LYS 2.7 43.8 + - - -
42A PRO 4.2 2.2 - - - -
84A CYS 4.1 2.5 - - - -
85A ARG 3.3 12.6 - - - +
86A GLU* 3.5 28.7 - - + -
87A THR* 3.5 7.4 - - - +
95A CYS* 3.6 22.9 - - + -
96A ALA* 1.3 77.4 - - - +
98A LYS* 1.3 61.6 + - - +
99A THR* 3.9 2.1 + - - -
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Residues in contact with LYS 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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26A CYS* 3.7 0.5 - - - -
83A ASP 3.4 6.6 - - - +
84A CYS* 3.5 2.9 - - - -
85A ARG* 2.7 38.3 + - + +
86A GLU 5.5 0.9 - - - +
87A THR* 3.4 12.2 - - + +
97A TYR* 1.3 73.9 - - - +
99A THR* 1.3 66.7 + - - +
100A THR* 3.4 24.0 + - - +
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Residues in contact with THR 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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20A ALA* 3.8 13.5 - - + +
22A SER 3.7 17.7 - - - +
23A SER* 3.2 23.9 + - - -
25A TYR* 3.9 3.6 - - + -
26A CYS* 3.1 31.5 + - - +
82A THR* 3.5 25.6 - - + -
97A TYR 3.9 1.0 + - - -
98A LYS* 1.3 78.7 + - - +
100A THR* 1.3 63.3 + - - +
101A GLN* 4.1 2.4 + - + +
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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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82A THR* 3.4 2.7 - - - -
83A ASP* 2.8 56.7 + - - +
98A LYS* 3.4 31.6 + - - +
99A THR* 1.3 72.6 + - - +
101A GLN* 1.3 69.0 + - - +
102A ALA* 3.8 5.3 + - + +
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Residues in contact with GLN 101 (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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19A ALA* 3.5 18.1 - - + +
20A ALA* 2.8 37.1 - - + +
48A HIS* 3.7 2.2 + - - -
80A SER* 2.8 23.0 + - - -
81A ILE 3.2 11.6 + - - +
82A THR* 2.7 30.8 + - - +
99A THR* 4.0 3.6 + - + +
100A THR* 1.3 77.3 - - - +
102A ALA* 1.3 72.8 + - - +
103A ASN* 4.7 4.3 + - - +
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Residues in contact with ALA 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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80A SER* 3.6 1.2 - - - -
81A ILE* 2.8 40.1 + - + +
83A ASP* 5.1 2.7 - - - +
100A THR* 4.8 6.5 - - + +
101A GLN* 1.3 84.2 - - - +
103A ASN* 1.3 66.4 + - - +
104A LYS* 4.0 23.1 - - + +
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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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78A THR* 4.0 20.4 + - + +
79A MET* 3.2 6.6 - - - +
80A SER* 3.6 28.1 - - - +
101A GLN* 4.7 4.0 + - - +
102A ALA* 1.3 79.5 - - - +
104A LYS* 1.3 65.3 + - - +
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Residues in contact with LYS 104 (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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78A THR* 3.6 12.3 - - - -
79A MET* 2.7 30.7 + - - +
81A ILE* 3.8 27.7 - - + +
83A ASP* 3.6 18.4 + - - -
102A ALA* 4.0 9.5 - - + +
103A ASN* 1.3 85.1 - - - +
105A HIS* 1.3 66.0 + - - +
106A ILE* 3.7 5.3 + - - +
123A SER* 3.6 29.0 + - - -
124A VAL* 3.2 25.8 - - - +
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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