Contacts of the strand formed by residues 135 - 147 (chain B) in PDB entry 4R95
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 GLY 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PRO* 4.4 0.2 - - - +
132B TYR* 2.8 48.3 + - - +
133B THR 3.3 2.0 - - - -
134B GLN* 1.3 77.8 - - - +
136B LYS* 1.4 67.4 + - - +
167B ASP* 3.1 16.8 - - - -
168B LYS* 4.3 2.2 - - - -
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU 4.9 9.3 + - - -
275A LYS 6.3 0.2 - - - -
276A MET* 5.0 8.1 - - - +
304A ALA* 4.6 17.8 - - - +
129B TYR* 3.7 29.7 + - + +
130B VAL 3.5 7.6 - - - +
131B PRO* 3.9 18.2 - - + -
132B TYR* 3.5 6.6 - - - -
135B GLY* 1.4 79.5 - - - +
137B TRP* 1.3 63.6 + - - +
138B GLU* 6.2 0.2 - - + -
166B SER* 3.3 6.1 - - - -
167B ASP* 2.8 58.3 + - + +
169B PHE* 3.8 3.6 - - - +
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Residues in contact with TRP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 3.8 31.2 - - + -
100B ALA* 3.8 13.6 - - + +
128B VAL* 3.6 20.6 - - + -
129B TYR* 4.3 0.3 - - - -
130B VAL* 2.7 77.0 + - + +
132B TYR* 4.0 8.5 - + - -
136B LYS* 1.3 75.2 - - - +
138B GLU* 1.3 63.6 + - - +
139B GLY* 4.4 2.7 - - - -
161B ALA* 3.4 34.5 - - + -
163B ILE* 3.8 22.7 - - + -
165B GLU 3.6 6.5 - - - +
166B SER* 4.5 0.2 - - - -
169B PHE* 3.5 39.0 - + + -
179B ILE* 4.8 6.6 - - + +
502B 3KW 5.3 5.5 - - + +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LYS* 3.0 41.2 + - - -
128B VAL 3.3 13.8 - - - +
129B TYR* 3.9 14.3 - - + +
136B LYS* 6.2 0.7 - - + -
137B TRP* 1.3 80.4 - - - +
139B GLY* 1.3 64.9 + - - +
163B ILE* 3.5 4.0 - - - -
164B THR* 2.9 26.4 + - - +
165B GLU* 2.8 42.6 + - + +
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY* 3.3 5.4 - - - -
128B VAL* 2.9 44.1 + - - +
137B TRP* 4.3 1.5 - - - -
138B GLU* 1.3 78.6 - - - +
140B GLU* 1.3 64.6 + - - +
162B ALA 3.1 15.5 - - - -
163B ILE* 4.2 0.2 - - - -
164B THR* 3.9 8.7 - - - -
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 2.7 38.6 + - - +
121B TYR* 5.8 0.7 - - - +
123B ASP* 5.7 3.1 - - - +
126B LYS 3.7 7.2 - - - +
127B GLY* 5.2 3.4 - - - -
139B GLY* 1.3 78.1 - - - +
141B LEU* 1.3 65.5 + - - +
160B ILE 3.7 0.7 - - - +
161B ALA* 4.4 1.3 - - - -
162B ALA* 2.8 38.3 + - - +
164B THR* 4.1 20.6 + - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 4.7 3.2 + - - -
123B ASP* 3.7 8.1 - - - +
124B LEU* 3.1 34.3 + - + +
125B ARG 4.0 2.1 + - - -
126B LYS* 2.9 44.7 + - + +
127B GLY 4.2 3.6 - - - +
128B VAL* 3.9 22.4 - - + -
140B GLU* 1.3 74.9 - - - +
142B GLY* 1.3 57.5 + - - +
159B ASN* 5.8 0.2 - - + -
160B ILE 3.7 3.8 - - - +
161B ALA* 4.1 15.5 - - + +
189B ARG 4.8 0.9 - - - +
190B PRO* 3.7 23.8 - - + -
194B LEU* 3.6 36.3 - - + -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 4.4 9.6 - - - -
122B ARG 3.0 15.5 - - - -
124B LEU* 3.8 10.3 - - - +
141B LEU* 1.3 76.6 - - - +
143B THR* 1.3 64.8 + - - +
159B ASN* 3.4 7.6 - - - +
160B ILE* 2.8 32.8 + - - -
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TYR* 5.0 0.2 - - - -
121B TYR* 3.6 4.1 - - - -
122B ARG* 2.8 47.5 + - - +
124B LEU* 4.1 16.8 - - + -
142B GLY* 1.3 74.1 - - - -
144B ASP* 1.3 64.7 + - - +
157B ARG* 3.2 29.7 + - + -
158B ALA 3.2 13.0 - - - +
159B ASN* 3.4 25.1 - - - +
160B ILE* 4.5 2.0 - - - +
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B GLY* 3.3 12.7 - - - +
113B TYR* 2.5 28.0 + - - +
118B SER* 2.8 24.8 + - - -
120B THR* 2.6 30.3 + - - -
121B TYR* 3.6 10.0 - - - -
143B THR* 1.3 73.9 + - - +
145B LEU* 1.3 72.6 + - - +
146B VAL* 3.6 3.5 - - - +
157B ARG* 3.5 13.1 - - - +
158B ALA 3.0 31.2 + - - +
160B ILE* 3.6 14.0 - - + +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B THR 4.0 0.3 - - - +
81B VAL* 3.4 3.6 - - - -
82B GLY 2.9 28.6 + - - +
83B SER* 4.0 9.4 - - - +
120B THR* 3.9 32.5 - - + +
144B ASP* 1.3 79.3 + - - +
146B VAL* 1.3 59.2 + - - +
155B THR* 3.8 21.5 - - + -
156B VAL 3.4 4.3 - - - +
157B ARG* 3.8 39.0 - - + +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 3.6 29.6 - - + -
80B THR 3.4 10.8 - - - +
81B VAL* 4.1 2.5 - - + -
99B PHE* 3.8 26.2 - - + -
144B ASP 3.6 12.1 - - - +
145B LEU* 1.3 79.4 - - - +
147B SER* 1.4 68.5 + - - +
154B VAL 4.2 0.3 - - - +
155B THR* 3.5 1.3 - - - -
156B VAL* 2.8 38.4 + - - +
158B ALA* 4.0 12.1 - - + -
160B ILE* 3.9 12.8 - - + -
197B PHE* 3.8 17.4 - - + -
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 3.4 8.3 - - - +
80B THR* 2.9 43.2 + - - +
145B LEU 5.4 0.2 - - - -
146B VAL* 1.4 75.2 + - - +
148B ILE* 1.3 66.1 + - - +
149B PRO* 4.0 4.5 - - - -
154B VAL 3.7 11.7 - - - -
155B THR* 2.9 28.5 + - - +
197B PHE* 6.1 0.7 - - - -
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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