Contacts of the strand formed by residues 135 - 143 (chain B) in PDB entry 4NZD
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 LEU 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 5.3 1.1 - - + -
101B PRO* 4.6 13.5 - - + -
123B TYR* 3.9 34.3 - - + -
131B LEU* 3.7 39.0 - - + +
133B GLY 3.5 0.2 - - - -
134B LYS* 1.3 89.3 - - + +
136B GLN* 1.3 61.2 + - - +
137B TYR* 4.1 13.0 - - + +
160B ASP* 3.1 38.4 + - - +
183B ALA* 4.9 4.7 - - + -
184B GLY 3.4 12.1 - - - +
185B PRO* 4.7 6.1 - - + -
186B MET* 3.3 5.8 - - - +
191B TYR* 6.4 0.4 - - + -
311B CL 4.0 14.6 - - + -
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Residues in contact with GLN 136 (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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135B LEU* 1.3 74.4 - - - +
137B TYR* 1.3 69.9 + - - +
156B LEU* 3.6 26.5 - - + +
157B ILE 3.6 11.9 - - - +
158B SER* 3.8 16.0 + - - -
159B VAL 4.7 0.4 - - - -
183B ALA* 3.5 1.9 - - - +
184B GLY 2.9 36.8 + - - +
185B PRO 4.3 0.4 - - - +
186B MET* 3.6 25.2 - - + +
187B PRO* 3.6 28.9 - - - +
195B TRP* 3.6 21.9 - - + -
307B CL 3.7 11.9 - - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 4.2 9.6 - - + -
119B TRP* 3.5 40.6 + + + -
121B SER* 4.3 10.8 + - - -
135B LEU* 4.1 14.9 - - + +
136B GLN* 1.3 78.3 - - - +
138B GLU* 1.3 58.0 + - - +
156B LEU* 3.6 5.2 - - - +
157B ILE* 2.7 47.3 + - + +
159B VAL 4.0 10.1 - - - -
160B ASP* 3.2 26.8 + - - -
161B SER 3.4 22.0 - - - -
162B ARG* 4.5 6.1 - - - +
181B VAL* 4.4 3.8 - - + -
182B ARG 3.3 16.8 - - - +
183B ALA* 3.5 22.9 - - + -
195B TRP* 4.1 4.0 - - - -
311B CL 3.5 14.4 - - - +
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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
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137B TYR* 1.3 76.3 - - - +
139B LEU* 1.3 73.9 + - - +
154B ARG* 3.3 29.5 + - - +
155B LYS 3.4 16.1 + - - +
156B LEU* 4.3 8.6 + - + +
181B VAL* 3.4 6.1 - - - +
182B ARG* 2.8 69.4 + - + -
195B TRP* 3.7 24.8 + - + -
198B TRP* 3.6 5.1 - - + -
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Residues in contact with LEU 139 (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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117B ILE* 4.2 10.1 - - + -
119B TRP* 3.9 16.6 - - + -
138B GLU* 1.3 76.8 - - - +
140B GLN* 1.3 61.3 + - - +
141B TYR* 4.6 9.0 - - + -
153B ARG 4.5 0.2 - - - -
154B ARG* 3.2 10.1 - - - +
155B LYS* 2.8 45.8 + - + +
157B ILE* 4.5 14.6 - - + -
164B VAL* 4.2 17.9 - - + -
166B LEU* 4.0 27.6 - - + -
179B LEU* 4.8 7.2 - - + -
180B GLN 3.5 2.7 - - - +
181B VAL* 3.5 36.6 - - + -
198B TRP* 4.2 0.7 - - - -
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Residues in contact with GLN 140 (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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139B LEU* 1.3 75.5 - - - +
141B TYR* 1.3 64.3 + - - +
152B PRO* 3.6 33.4 + - + +
153B ARG 3.3 7.6 - - - +
154B ARG* 3.1 37.0 - - + +
179B LEU* 3.2 3.1 - - - +
180B GLN* 2.8 69.4 + - + +
198B TRP* 3.6 28.4 + - + +
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Residues in contact with TYR 141 (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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139B LEU* 4.6 5.4 - - + -
140B GLN* 1.3 79.2 - - - +
142B ARG* 1.3 63.7 + - - +
152B PRO* 3.4 3.3 - - - +
153B ARG* 3.0 72.5 + - + +
154B ARG 5.3 0.9 + - - -
155B LYS* 4.6 23.6 - - + +
166B LEU* 4.6 12.1 - - + +
170B GLU* 3.9 29.0 + - + +
171B PHE* 3.8 27.6 - + + -
177B TYR* 4.3 12.6 - + + -
178B GLU 3.0 13.9 - - - +
179B LEU* 3.8 26.5 - - + -
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Residues in contact with ARG 142 (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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141B TYR* 1.3 77.7 - - - +
143B ASN* 1.3 67.0 + - - +
144B ARG* 3.6 2.2 + - + +
150B VAL 5.5 4.9 - - - +
151B SER 5.4 1.6 - - - +
152B PRO* 4.3 26.5 - - + +
177B TYR* 3.5 10.3 - - - -
178B GLU* 2.8 71.1 + - + +
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Residues in contact with ASN 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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142B ARG* 1.3 77.2 - - - +
144B ARG* 1.3 60.5 + - - +
145B GLY* 3.3 14.3 + - - +
146B ASP* 2.9 35.7 + - - +
172B ARG* 2.9 37.0 - - - +
175B SER* 3.3 34.4 + - - -
176B SER 2.7 28.3 + - - +
177B TYR* 3.8 18.4 - - + +
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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