Contacts of the strand formed by residues 152 - 163 (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 VAL 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B TYR* 4.4 9.4 - - - +
148B VAL* 3.3 7.4 - - - +
149B ARG* 2.8 38.6 + - - +
150B ASP* 3.2 3.3 - - + +
151B GLY* 1.3 83.3 - - - +
153B LEU* 1.3 60.5 + - - +
154B LYS* 4.8 8.7 - - - -
176B THR* 4.0 20.2 - - + -
177B TYR 3.6 10.1 - - - +
178B LYS* 4.2 17.5 - - + -
185B LEU* 5.2 0.9 - - - -
73D GLU* 3.6 32.1 - - + +
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Residues in contact with LEU 153 (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 36.1 + - + -
79B PHE* 3.6 32.8 - - + -
146B LEU* 4.0 12.1 - - + -
147B TYR* 3.4 34.3 - - - +
148B VAL* 4.1 5.6 - - + +
152B VAL* 1.3 75.3 - - - +
154B LYS* 1.3 63.7 + - - +
176B THR* 3.6 3.5 - - - +
177B TYR* 2.7 51.1 + - + +
186B PRO* 3.9 22.9 - - + -
187B ASP 6.0 0.2 - - - +
189B HIS* 4.9 1.6 - - + -
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Residues in contact with LYS 154 (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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145B LYS 3.8 0.4 - - - +
146B LEU* 3.1 7.8 - - - +
147B TYR* 2.8 61.3 + - + +
149B ARG* 4.0 38.1 - - + +
152B VAL* 4.8 8.1 - - + +
153B LEU* 1.3 79.3 - - - +
155B GLY* 1.3 58.1 + - - +
156B ASP* 4.7 2.7 - - - +
175B THR 3.3 6.7 - - - +
176B THR* 3.0 34.3 + - + +
177B TYR* 4.3 4.5 - - - -
124E ASN* 4.7 15.0 + - - +
126E PRO* 5.8 7.8 - - - +
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Residues in contact with GLY 155 (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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144B GLU* 3.3 24.6 - - - +
145B LYS 3.2 8.7 - - - -
146B LEU* 4.4 0.7 - - - -
154B LYS* 1.3 74.9 - - - +
156B ASP* 1.3 63.2 + - - +
157B VAL* 5.6 0.2 - - - -
173B PHE* 3.9 2.1 - - - +
174B LYS* 3.7 1.0 - - - -
175B THR* 2.8 42.0 + - - -
177B TYR* 4.0 5.4 - - - -
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Residues in contact with ASP 156 (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* 2.7 41.8 + - - +
144B GLU* 4.4 0.2 - - - -
145B LYS* 2.9 40.4 + - + +
147B TYR* 2.5 33.9 + - + -
154B LYS* 4.3 2.3 - - - +
155B GLY* 1.3 83.7 + - - +
157B VAL* 1.3 60.4 + - - +
173B PHE 3.4 6.1 - - - +
174B LYS* 3.5 27.6 - - + +
175B THR 4.3 1.0 + - - +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LYS* 3.7 18.4 - - - +
158A ASN* 3.7 7.2 + - - -
63B KZ4 3.6 21.3 - - + -
142B SER* 4.1 9.6 - - - -
143B THR 3.4 23.1 - - - +
144B GLU* 3.7 20.2 - - + -
145B LYS* 4.7 4.0 - - - +
155B GLY 5.5 0.4 - - - +
156B ASP* 1.3 77.6 - - - +
158B ASN* 1.3 63.4 + - - +
159B THR 3.7 7.6 + - - +
171B CYS 3.8 0.2 - - - +
172B ASP* 3.7 0.3 - - - -
173B PHE* 2.8 51.3 + - + +
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Residues in contact with ASN 158 (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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145A LYS* 4.0 22.8 + - + +
156A ASP* 3.9 26.4 + - + +
157A VAL* 5.3 1.1 - - - +
158A ASN* 3.3 36.8 + - - +
174A LYS* 3.3 27.9 - - - +
188A TYR* 4.5 0.3 + - - -
145B LYS* 5.3 2.8 - - - +
157B VAL* 1.3 77.0 - - - +
159B THR* 1.3 66.8 + - - +
170B ARG* 4.3 6.3 - - - +
171B CYS 3.5 13.1 + - - +
172B ASP* 4.4 11.7 + - - +
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Residues in contact with THR 159 (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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145A LYS* 4.3 3.4 - - - +
188A TYR* 4.1 9.8 + - - -
63B KZ4 4.3 9.0 + - + -
139B TRP* 3.4 28.8 - - + -
140B GLU* 4.0 8.0 + - - +
141B PRO 4.5 0.7 + - - -
142B SER* 4.0 25.5 - - - -
157B VAL* 3.7 3.7 - - + +
158B ASN* 1.3 80.2 - - - +
160B ALA* 1.3 83.9 + - - +
170B ARG* 3.6 3.6 - - - +
171B CYS 3.0 23.0 + - - +
173B PHE* 3.8 23.1 - - + -
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Residues in contact with ALA 160 (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* 6.1 1.1 - - + -
188A TYR* 3.9 26.9 + - + -
139B TRP* 3.5 9.6 - - - -
140B GLU* 3.1 26.9 + - - +
159B THR* 1.3 94.2 + - - +
161B LEU* 1.3 59.8 + - - +
168B HIS* 4.0 17.5 - - + -
169B TYR 3.4 12.1 - - - +
170B ARG* 4.1 9.9 - - + +
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Residues in contact with LEU 161 (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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55B ASP* 3.6 24.9 - - + +
56B ILE* 4.8 5.6 - - + -
95B TYR* 4.1 16.4 - - + +
136B THR* 4.0 23.8 - - + -
138B LYS 3.3 22.0 - - - +
139B TRP* 3.4 55.8 - - + +
160B ALA* 1.3 72.6 - - - +
162B SER* 1.3 65.7 + - - +
163B LEU 3.8 0.3 + - - -
168B HIS* 3.3 6.4 - - - -
169B TYR* 2.8 46.3 + - + +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 3.5 4.3 - - - -
137B VAL* 2.6 44.5 + - - +
138B LYS* 2.8 25.0 + - - +
140B GLU* 4.0 19.8 + - - +
160B ALA 4.1 1.0 + - - -
161B LEU* 1.3 74.3 - - - +
163B LEU* 1.3 61.5 + - - +
166B GLY* 5.8 0.3 - - - -
167B GLY 3.6 9.2 + - - -
168B HIS* 4.1 7.8 + - - -
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Residues in contact with LEU 163 (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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130B PRO* 3.9 25.1 - - + -
135B ARG* 3.3 17.5 - - + +
136B THR* 4.1 10.8 - - + -
137B VAL* 3.4 8.5 - - - +
161B LEU 4.0 4.3 - - - +
162B SER* 1.3 85.3 + - - +
164B GLU* 1.3 70.2 + - - +
165B GLY 4.7 1.8 - - - +
166B GLY* 3.1 23.4 + - - +
167B GLY 3.1 15.9 + - - +
168B HIS 4.5 9.9 - - - +
169B TYR* 3.8 29.8 - - + -
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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