Contacts of the strand formed by residues 168 - 179 (chain B) in PDB entry 6NQN
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 HIS 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A TYR* 4.3 24.5 - - + +
148A VAL 5.0 6.9 + - - -
149A ARG* 2.9 29.0 + - - +
188A TYR* 3.3 41.3 - + + -
96B GLU* 3.7 0.5 - - - +
140B GLU* 2.6 37.5 + - + -
160B ALA* 4.0 11.4 - - + -
161B LEU 3.3 11.9 - - - -
162B SER* 4.1 7.8 - - - -
163B LEU* 4.5 7.6 - - - +
167B GLY* 1.3 93.6 - - - -
169B TYR* 1.3 58.3 + - - +
170B ARG* 4.1 0.9 - - + -
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Residues in contact with TYR 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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95B TYR* 3.2 37.9 - + + +
96B GLU* 3.5 11.9 - - + -
97B ASP* 2.5 51.7 + - + -
125B PHE* 3.5 14.2 - - - -
130B PRO* 3.8 25.1 - - + -
131B VAL* 3.5 20.5 - - + +
136B THR* 4.9 0.9 - - + -
160B ALA* 3.4 1.1 - - - -
161B LEU* 2.8 48.3 + - + +
163B LEU* 3.8 23.8 - - + -
168B HIS* 1.3 72.7 - - - +
170B ARG* 1.3 63.6 + - - +
171B CYS* 4.9 1.6 - - - +
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Residues in contact with ARG 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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147A TYR* 2.9 30.3 + - + +
149A ARG* 3.5 15.8 - - - +
156A ASP* 2.9 22.9 + - - +
174A LYS* 3.1 44.1 - - - +
95B TYR* 3.5 6.2 - - - +
96B GLU* 2.7 76.3 + - + +
158B ASN* 4.3 6.8 + - - +
159B THR 3.6 12.6 - - - +
160B ALA* 4.1 7.9 - - + +
168B HIS 5.1 0.7 - - - +
169B TYR* 1.3 74.5 - - - +
171B CYS* 1.3 61.1 + - - +
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Residues in contact with CYS 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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93B MET* 3.7 14.4 - - - -
94B ASN 3.6 10.5 - - - -
95B TYR* 3.6 40.4 - - + -
139B TRP* 4.0 9.9 - - + -
157B VAL 3.8 0.9 - - - +
158B ASN* 3.5 5.3 - - - +
159B THR* 3.0 35.2 + - - +
169B TYR 3.9 0.4 + - - +
170B ARG* 1.3 76.7 - - - +
172B ASP* 1.3 62.4 + - - +
173B PHE* 3.3 30.3 - - + -
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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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158A ASN* 3.5 19.9 + - - +
170A ARG* 4.9 0.2 + - - -
172A ASP* 3.7 14.0 - - - +
92B SER 3.5 4.9 - - - +
93B MET* 3.6 0.2 - - - -
94B ASN* 2.9 45.7 + - + +
157B VAL 3.7 2.2 - - - -
158B ASN* 4.4 11.4 + - - +
171B CYS* 1.3 71.0 - - - +
173B PHE* 1.3 70.3 + - - +
174B LYS* 3.2 32.6 + - - +
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Residues in contact with PHE 173 (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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59B THR* 3.4 31.9 - - + -
63B KZ4 3.7 27.8 - + + -
91B ARG* 4.0 20.2 - - - -
92B SER 3.6 3.6 - - - -
93B MET* 3.8 15.0 - - + -
139B TRP* 3.8 19.5 - + - -
155B GLY 4.4 1.1 - - - +
156B ASP* 3.4 5.9 - - - -
157B VAL* 2.8 46.4 + - + +
159B THR* 3.8 17.5 - - + -
171B CYS* 3.3 29.6 - - - -
172B ASP* 1.3 83.8 + - - +
174B LYS* 1.3 62.1 + - - +
175B THR* 4.2 4.7 - - - +
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Residues in contact with LYS 174 (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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170A ARG* 4.6 10.0 - - - +
172A ASP* 4.1 11.3 + - - -
91B ARG* 3.2 1.5 - - - +
92B SER* 2.9 42.2 + - - +
155B GLY 3.8 1.8 - - - -
156B ASP* 3.5 24.5 - - - +
172B ASP* 3.2 34.0 + - - +
173B PHE* 1.3 76.8 - - - +
175B THR* 1.3 62.0 + - - +
98E GLY* 6.1 1.1 - - - +
124E ASN* 3.0 19.6 + - - +
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Residues in contact with THR 175 (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 TRP* 4.2 5.8 - - + -
90B GLU 3.3 12.8 - - - +
91B ARG* 2.8 35.3 + - + +
144B GLU* 4.6 1.8 + - - -
154B LYS* 3.3 8.5 - - - +
155B GLY 2.8 37.3 + - - -
156B ASP* 4.3 1.1 + - - +
173B PHE* 4.8 4.2 - - - +
174B LYS* 1.3 72.1 + - - +
176B THR* 1.3 68.6 + - - +
177B TYR* 3.5 43.0 + - + +
124E ASN* 4.3 0.2 - - - -
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Residues in contact with THR 176 (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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88B SER 4.0 0.2 - - - +
89B TRP* 3.1 6.8 - - - +
90B GLU* 2.9 36.2 + - - +
152B VAL* 4.0 19.7 - - + -
153B LEU 3.6 3.8 - - - +
154B LYS* 3.0 29.3 + - + +
175B THR* 1.3 71.5 - - - +
177B TYR* 1.3 63.5 + - - +
178B LYS* 3.8 32.3 + - + +
124E ASN* 2.7 25.3 + - - +
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Residues in contact with TYR 177 (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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66B ARG* 2.9 32.3 + - + -
78B TYR* 3.5 10.3 + - + -
79B PHE* 3.4 44.0 - + + -
87B TYR* 4.1 6.7 - + + -
88B SER 3.7 3.6 - - - +
89B TRP* 3.7 23.3 - + + -
91B ARG* 4.9 0.2 - - - -
144B GLU* 2.6 29.2 + - - -
146B LEU* 4.0 7.9 - - + -
152B VAL* 3.6 6.2 - - - +
153B LEU* 2.7 54.2 + - + +
154B LYS 4.3 0.7 - - - -
155B GLY 4.0 10.8 - - - -
175B THR* 3.5 23.5 + - + +
176B THR* 1.3 73.0 - - - +
178B LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 178 (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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78B TYR* 3.7 1.8 - - - -
87B TYR* 3.4 3.5 - - - -
88B SER* 2.9 46.6 + - - +
89B TRP* 5.9 0.2 - - - -
90B GLU* 2.8 30.3 + - - +
152B VAL* 4.2 15.7 - - + -
176B THR* 3.8 24.2 - - + +
177B TYR* 1.3 78.8 - - - +
179B ALA* 1.3 67.7 + - - +
180B LYS* 4.8 1.0 - - - +
73D GLU* 4.8 14.8 + - - +
19E ASN* 3.9 19.2 + - - +
125E PHE 4.9 3.0 + - - -
127E ALA* 6.1 2.0 - - - +
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Residues in contact with ALA 179 (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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78B TYR* 2.9 27.0 + - + +
82B SER* 3.3 24.9 - - - +
87B TYR* 3.6 9.2 - - - -
178B LYS* 1.3 76.8 - - - +
180B LYS* 1.3 63.7 + - - +
181B LYS 3.2 21.2 + - - +
183B VAL* 4.1 7.9 - - + -
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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