Contacts of the strand formed by residues 128 - 136 (chain A) in PDB entry 2G5T
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASP* 5.6 0.5 + - - -
117A GLU* 2.7 30.7 + - - -
120A TYR* 3.3 30.1 - + + +
121A VAL 3.2 16.2 - - - +
122A LYS* 3.7 9.2 - - - -
123A GLN* 3.9 8.5 - - - +
126A HIS 3.6 21.5 - - - -
127A SER* 1.3 77.4 - - - +
129A THR* 1.3 80.1 + - - +
130A ALA* 4.3 3.4 - - + -
132A TYR* 3.7 18.8 + - - -
152A THR 5.7 0.7 - - - -
153A GLN 3.3 23.4 - - - +
154A TRP* 5.0 19.2 - + - -
211A TYR* 3.7 5.1 - + - -
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Residues in contact with THR 129 (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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119A ASN 4.3 0.4 - - - -
121A VAL* 2.9 47.9 + - - +
123A GLN* 6.2 3.8 - - + +
128A TYR* 1.3 83.6 - - - +
130A ALA* 1.3 66.4 + - - +
151A ASN* 4.1 22.2 + - + +
152A THR 3.2 11.9 - - - +
153A GLN* 4.2 18.6 - - + -
211A TYR* 5.2 3.4 - - - +
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Residues in contact with ALA 130 (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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117A GLU* 3.9 17.5 - - + -
118A TYR 3.3 13.7 - - - +
119A ASN* 3.5 7.2 - - - -
120A TYR* 4.0 7.6 - - - -
128A TYR* 4.3 4.0 - - + -
129A THR* 1.3 81.0 - - - +
131A SER* 1.3 63.1 + - - +
132A TYR* 3.6 26.2 - - + +
150A ASN 4.2 0.2 - - - -
151A ASN* 3.4 5.6 + - - +
152A THR* 3.0 27.3 + - - -
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Residues in contact with SER 131 (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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117A GLU* 3.6 0.7 - - - -
118A TYR* 2.7 64.4 + - - -
119A ASN* 3.1 18.6 + - - +
130A ALA* 1.3 75.0 - - - +
132A TYR* 1.3 66.7 + - - +
149A PRO 4.7 0.2 - - - -
150A ASN* 2.8 35.0 + - - +
151A ASN 4.5 0.7 + - - -
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Residues in contact with TYR 132 (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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115A LEU* 3.9 24.7 - - + -
116A LEU 3.1 14.8 - - - +
117A GLU* 2.8 42.9 + - + -
118A TYR* 4.0 4.5 + - - -
128A TYR* 3.7 15.6 + - - -
130A ALA* 3.6 23.6 - - + -
131A SER* 1.3 76.4 - - - +
133A ASP* 1.3 69.2 + - - +
147A ARG* 5.3 1.9 - - - +
148A ILE* 4.0 45.3 + - + +
149A PRO 4.8 0.8 + - - -
152A THR* 4.0 17.4 + - + -
153A GLN 5.8 0.2 - - - -
154A TRP* 5.3 3.5 - - - -
155A VAL* 3.9 36.7 + - + +
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Residues in contact with ASP 133 (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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98A PHE* 3.2 33.8 - - + -
100A HIS* 5.4 0.9 - - - -
114A ILE 3.7 0.3 - - - +
115A LEU* 3.7 2.4 - - - +
116A LEU* 2.8 38.1 + - + +
118A TYR* 3.6 16.6 + - + -
132A TYR* 1.3 79.0 - - - +
134A ILE* 1.3 65.7 + - - +
142A LEU* 4.2 19.9 - - + +
143A ILE 4.7 9.5 - - - +
147A ARG* 5.1 15.0 + - - +
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Residues in contact with ILE 134 (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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113A PHE* 3.9 23.1 - - + -
114A ILE 3.5 9.2 - - - +
115A LEU* 3.9 14.6 - - + -
133A ASP* 1.3 76.4 - - - +
135A TYR* 1.3 60.7 + - - +
142A LEU* 3.8 4.3 - - - +
143A ILE* 2.9 54.1 + - + +
148A ILE* 4.1 16.8 - - + +
157A TRP* 4.2 3.6 - - + -
164A LEU* 3.3 33.4 - - + -
175A LYS* 4.9 1.3 - - + -
178A PRO* 3.9 24.9 - - + +
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Residues in contact with TYR 135 (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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90A LEU* 5.9 0.7 - - + -
94A THR* 3.6 10.6 - - + +
95A PHE* 3.7 35.2 - + + -
113A PHE* 3.4 6.6 - - - -
114A ILE* 2.9 43.1 + - + +
116A LEU* 4.8 3.6 - - + -
133A ASP 4.0 0.8 + - - -
134A ILE* 1.3 74.0 - - - +
136A ASP* 1.3 68.8 + - - +
137A LEU* 3.4 15.7 + - + -
140A ARG* 3.1 63.1 + - - +
141A GLN* 3.4 19.3 - - - -
142A LEU* 3.7 29.2 - - + -
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Residues in contact with ASP 136 (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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112A GLN* 4.0 3.3 - - - +
113A PHE* 3.4 30.7 - - + -
134A ILE 4.1 0.8 + - - -
135A TYR* 1.3 71.7 - - - +
137A LEU* 1.3 54.0 + - - +
138A ASN* 3.1 21.9 + - - +
139A LYS* 3.3 44.9 + - + +
140A ARG* 2.7 35.7 + - - -
141A GLN 3.0 15.7 + - - +
143A ILE* 4.8 8.2 - - + +
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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