Contacts of the strand formed by residues 164 - 172 (chain B) in PDB entry 3BN3
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 ASN 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B LEU 4.0 0.3 - - - +
128B ARG* 3.5 1.6 - - - -
129B GLY* 2.8 38.2 + - - +
163B ALA* 1.3 73.1 - - - +
165B PHE* 1.3 61.5 + - - +
166B SER* 4.2 1.5 + - - -
187B PRO* 3.9 25.9 - - + +
188B ARG 3.5 2.9 - - - -
189B GLU* 4.1 18.5 + - - +
201B NAG 1.5 64.3 + - - +
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Residues in contact with PHE 165 (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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94B LEU* 3.3 8.7 - - + +
97B LEU* 4.1 7.0 - - + -
107B PHE* 4.0 20.6 - + - -
109B LEU* 3.7 39.0 - - + -
127B LEU 3.2 12.1 - - - +
128B ARG* 3.5 39.3 - - + -
133B LEU* 3.9 11.4 - - + -
154B VAL* 4.6 4.0 - - + -
160B ASP* 4.6 5.4 - - - -
163B ALA* 3.8 14.6 - - + -
164B ASN* 1.3 75.7 - - - +
166B SER* 1.3 64.1 + - - +
187B PRO* 3.4 0.7 - - - +
188B ARG 2.7 41.0 + - - +
190B LEU* 3.6 33.7 - - + -
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Residues in contact with SER 166 (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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94B LEU* 3.8 7.8 - - - +
109B LEU* 5.6 0.5 - - - +
126B LEU* 3.7 4.2 - - - +
127B LEU* 2.8 47.1 + - - +
129B GLY 4.7 4.2 + - - -
164B ASN 5.2 1.4 + - - -
165B PHE* 1.3 76.8 - - - +
167B CYS* 1.3 67.1 + - - +
184B SER* 5.6 3.0 - - - -
185B SER* 3.4 23.1 - - - -
187B PRO* 4.3 10.8 - - - -
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Residues in contact with CYS 167 (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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92B VAL* 3.6 10.3 - - - +
93B GLU 4.3 3.6 - - - -
94B LEU* 4.3 6.3 - - + -
111B CYS* 2.1 55.9 - - + -
125B THR 3.1 14.1 - - - +
126B LEU* 3.6 7.4 - - + -
127B LEU* 4.3 4.3 - - - -
166B SER* 1.3 77.4 - - - +
168B ARG* 1.3 59.4 + - - +
184B SER* 3.2 6.2 - - - -
185B SER* 2.8 42.8 + - - -
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Residues in contact with ARG 168 (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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92B VAL* 4.5 2.2 - - - -
111B CYS* 5.1 0.4 - - - -
123B THR 3.8 1.3 - - - +
124B LEU* 3.3 6.9 - - - +
125B THR* 2.9 37.3 + - - +
127B LEU* 3.9 33.7 - - + +
132B GLU* 3.0 25.9 + - - -
135B ARG* 3.4 11.3 - - - +
167B CYS* 1.3 76.3 - - - +
169B ALA* 1.3 70.0 + - - +
170B GLU* 3.1 26.9 + - + +
182B GLU* 4.0 21.4 + - - -
183B ASN 3.4 11.0 - - - +
184B SER* 3.5 19.9 + - - +
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Residues in contact with ALA 169 (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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89B PRO* 3.8 13.8 - - + +
92B VAL* 3.7 25.3 - - + +
113B VAL* 3.8 22.4 - - + -
122B LEU* 4.9 2.2 - - + -
123B THR 3.6 3.8 - - - -
124B LEU* 4.3 7.0 - - + -
168B ARG* 1.3 73.6 - - - +
170B GLU* 1.3 62.9 + - - +
181B PHE 3.9 0.6 - - - +
182B GLU* 3.3 4.9 - - - +
183B ASN 2.8 31.1 + - - +
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Residues in contact with GLU 170 (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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121B SER 3.5 1.7 - - - +
122B LEU* 3.1 10.1 - - - +
123B THR* 2.9 47.0 + - - +
125B THR* 4.2 2.1 + - - -
135B ARG* 3.1 39.0 + - - -
168B ARG* 3.1 25.6 + - + +
169B ALA* 1.3 78.6 - - - +
171B LEU* 1.3 58.9 - - - +
172B ASP* 3.8 2.0 - - + +
180B LEU* 3.9 17.6 - - + +
181B PHE 3.5 4.7 - - - -
182B GLU* 3.7 25.9 - - + +
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Residues in contact with LEU 171 (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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86B PHE* 4.3 4.7 - - + -
87B GLN 3.3 30.5 - - - +
88B ARG* 4.2 6.1 - - - +
89B PRO* 4.2 7.2 - - + +
117B GLY* 3.4 33.7 - - - +
118B PRO 3.7 4.7 - - - +
121B SER* 3.6 25.8 - - - +
122B LEU* 4.0 12.8 - - + +
170B GLU* 1.3 70.1 - - - +
172B ASP* 1.3 57.1 + - - +
173B LEU* 3.5 27.0 + - + -
179B GLY 3.7 1.0 - - - +
180B LEU* 3.4 3.3 - - - -
181B PHE* 2.7 49.0 + - + +
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Residues in contact with ASP 172 (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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121B SER* 3.0 29.5 + - - +
170B GLU* 3.8 2.6 - - + +
171B LEU* 1.3 69.3 - - - +
173B LEU* 1.3 60.7 + - - +
174B ARG* 2.8 58.2 + - - +
175B PRO* 3.7 15.9 - - - +
176B HIS* 5.2 0.7 + - - -
179B GLY 4.2 0.2 - - - -
180B LEU* 3.8 11.2 - - + -
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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