Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 2EA3
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 ALA 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLY 3.6 2.0 + - - -
92A SER* 1.3 70.7 - - - +
94A VAL* 1.3 64.0 + - - +
95A CYS* 5.8 1.8 - - - -
105A CYS* 6.3 1.6 - - + -
106A GLY 3.4 10.3 - - - +
107A THR* 4.5 6.3 - - + +
143A ALA* 3.8 15.6 - - - +
144A GLY 4.6 2.3 + - - -
190A SO4 2.8 24.2 + - - +
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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
----------------------------------------------------------
92A SER 4.0 1.3 - - - +
93A ALA* 1.3 80.1 - - - +
95A CYS* 1.3 63.5 - - - +
105A CYS* 3.2 4.0 - - - +
106A GLY 2.8 38.3 + - - +
107A THR 4.1 4.9 - - - -
108A ILE* 3.7 39.5 - - + -
128A THR* 4.3 4.7 - - + -
130A VAL* 3.9 13.1 - - + +
141A LEU* 3.7 21.5 - - + -
142A LEU 3.2 15.5 - - - +
143A ALA* 4.0 11.7 - - + -
148A GLN* 4.4 6.3 - - + -
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Residues in contact with CYS 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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93A ALA* 5.8 1.8 - - - -
94A VAL* 1.3 75.0 - - - +
96A ARG* 1.3 61.1 + - - +
103A TRP* 3.3 36.4 - - + -
104A HIS 3.4 3.8 - - - -
105A CYS* 2.0 45.8 - - - -
130A VAL* 5.2 0.2 - - - -
140A SER 3.8 0.7 - - - +
141A LEU* 3.5 4.5 - - - -
142A LEU* 2.8 38.2 + - + +
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Residues in contact with ARG 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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95A CYS* 1.3 74.3 - - - +
97A SER* 1.3 64.0 + - - +
98A GLY* 3.3 12.9 - - - +
101A THR* 2.7 22.3 + - - -
102A GLY 3.3 20.2 + - - +
103A TRP* 3.3 9.9 - - - -
104A HIS* 2.8 52.5 + - - +
130A VAL* 3.7 15.1 - - + +
131A CYS 2.9 28.1 + - - -
132A ALA* 3.7 11.5 - - - +
136A ASP* 3.4 21.8 + - - -
140A SER 3.2 10.1 - - - +
141A LEU* 4.1 7.4 - - + -
151A THR* 3.4 27.1 - - - +
158A CYS* 3.9 1.8 - - - -
166A PHE* 3.9 13.5 - - + -
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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
----------------------------------------------------------
6A GLY* 3.4 15.8 - - - -
72A VAL* 3.5 22.7 - - - -
73A ASN 2.6 28.9 + - - -
75A TYR* 3.2 15.1 - - - -
96A ARG* 1.3 77.8 - - - +
98A GLY* 1.3 58.8 + - - +
102A GLY 3.5 4.5 - - - -
103A TRP* 4.0 5.6 - - - -
139A GLY* 3.5 4.9 - - - -
140A SER* 3.0 26.9 + - - +
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Residues in contact with GLY 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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6A GLY 3.4 9.2 - - - -
18A SER* 3.7 8.1 - - - -
75A TYR* 3.5 4.3 - - - -
96A ARG* 3.3 5.1 - - - +
97A SER* 1.3 77.8 + - - +
99A SER* 1.3 59.2 + - - -
102A GLY* 2.9 34.2 + - - -
136A ASP* 3.2 22.7 - - - -
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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