Contacts of the strand formed by residues 131 - 139 (chain A) in PDB entry 2YGE
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.0 0.2 - - - +
127A LEU* 3.0 19.2 + - + +
128A PHE* 3.5 29.7 - - - +
129A LEU 3.7 0.8 - - - -
130A VAL* 1.3 81.5 - - + +
132A ASP* 1.3 62.2 + - - +
133A ARG 3.4 14.1 - - - +
175A LEU* 4.0 18.2 - - + -
176A PHE 3.4 19.1 - - - +
177A LEU* 4.4 0.9 - - - -
178A LYS* 3.7 5.9 - - - +
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Residues in contact with ASP 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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20A ILE* 4.2 16.2 - - + -
128A PHE* 4.5 5.4 - - - -
131A ALA* 1.3 74.4 - - - +
133A ARG* 1.3 65.3 + - - +
151A ASN* 3.5 24.5 - - - +
152A ALA* 4.9 0.5 - - - +
176A PHE* 2.9 18.6 + - - +
177A LEU 4.4 3.1 - - - +
178A LYS* 3.9 19.5 - - + +
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Residues in contact with ARG 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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128A PHE* 4.6 1.7 - - - -
131A ALA* 3.4 8.2 - - - +
132A ASP* 1.3 87.9 + - - +
134A VAL* 1.3 68.4 + - - +
135A GLN* 3.5 14.1 - - - +
149A GLU* 2.8 30.9 + - + +
150A SER 3.4 14.1 - - - +
151A ASN* 4.5 10.3 - - + -
176A PHE* 3.0 67.4 + - + -
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Residues in contact with VAL 134 (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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127A LEU* 3.8 23.6 - - + -
128A PHE* 3.9 21.5 - - + -
133A ARG* 1.3 78.0 - - - +
135A GLN* 1.3 78.0 + - - +
136A VAL* 4.2 11.4 - - + -
148A TRP* 3.8 18.7 - - + +
149A GLU* 3.4 6.5 - - - +
150A SER* 3.0 38.2 + - - +
173A LEU* 5.1 1.6 - - + -
174A ARG 3.3 10.8 - - - +
175A LEU* 3.8 17.7 - - + -
176A PHE* 4.3 1.6 - - - -
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Residues in contact with GLN 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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133A ARG* 3.5 14.1 - - - +
134A VAL* 1.3 74.5 - - - +
136A VAL* 1.3 61.6 + - - +
137A ILE* 3.9 6.1 - - + +
147A ILE* 4.1 17.3 - - + +
148A TRP 3.2 4.7 - - - +
149A GLU* 3.3 44.9 + - + +
164A ASN* 4.9 1.2 + - - -
172A ILE 3.5 1.4 - - - +
173A LEU* 3.7 1.7 - - - -
174A ARG* 2.8 73.2 + - + +
176A PHE* 4.0 15.2 - - + -
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Residues in contact with VAL 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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84A MET* 3.9 29.2 - - + -
89A LEU* 3.9 12.2 - - + +
93A LEU* 4.0 4.7 - - + -
124A PHE* 3.7 27.6 - - + -
134A VAL* 4.2 3.1 - - + -
135A GLN* 1.3 75.4 - - - +
137A ILE* 1.3 61.7 + - - +
138A SER* 4.1 1.1 + - - -
146A TYR 3.6 1.7 - - - +
147A ILE* 3.5 1.6 - - - -
148A TRP* 2.7 64.0 + - + +
171A THR* 3.9 11.7 - - + -
172A ILE 3.4 2.7 - - - -
173A LEU* 4.1 11.0 - - + -
1215A GDM 4.3 1.8 - - - -
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Residues in contact with ILE 137 (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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135A GLN* 4.4 7.0 - - + +
136A VAL* 1.3 76.2 - - - +
138A SER* 1.3 63.7 + - - +
145A GLN* 3.5 19.1 - - + +
146A TYR 3.5 4.3 - - - +
147A ILE* 4.3 11.9 - - + -
161A ASP* 3.4 22.0 - - - +
164A ASN* 3.5 25.6 - - + +
167A ILE* 3.7 7.2 - - + +
171A THR* 3.2 3.1 - - - +
172A ILE* 2.7 60.1 + - + +
174A ARG* 3.6 36.8 - - + +
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Residues in contact with SER 138 (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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84A MET* 2.8 55.1 + - - +
89A LEU* 4.3 11.7 - - - -
136A VAL* 4.7 0.2 - - - -
137A ILE* 1.3 77.7 - - - +
139A LYS* 1.3 61.1 + - - +
140A SER 4.2 0.4 - - - -
144A GLU 3.9 2.3 - - - +
145A GLN* 3.4 4.0 - - - -
146A TYR* 3.1 32.5 + - - +
167A ILE* 4.0 1.6 - - - -
170A GLY 3.3 3.4 + - - -
171A THR* 2.9 18.7 + - - -
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Residues in contact with LYS 139 (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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58A THR* 5.7 3.0 - - - +
83A GLY* 3.7 5.4 - - - -
138A SER* 1.3 73.6 + - - +
140A SER* 1.3 83.2 + - - +
141A ASN* 3.9 11.5 + - - +
143A ASP 2.9 21.5 + - - +
144A GLU* 4.4 3.6 - - - +
145A GLN* 3.6 27.6 - - + +
167A ILE* 3.2 36.1 - - + +
168A GLY 3.7 13.7 + - - +
169A ARG* 3.6 4.7 - - - +
170A GLY 2.9 34.9 + - - +
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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