Contacts of the strand formed by residues 152 - 163 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A TYR* 4.1 9.4 - - - +
148A VAL* 3.4 7.2 - - - +
149A ARG 2.8 40.2 + - - +
150A ASP* 4.1 11.2 - - + +
151A GLY* 1.3 83.3 - - - +
153A LEU* 1.3 63.1 + - - +
154A LYS* 4.8 5.6 - - - -
176A THR* 3.8 25.6 - - + -
177A TYR 3.4 10.3 - - - +
178A LYS* 4.1 22.4 - - + -
185A LEU* 4.8 4.7 - - - -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.8 40.4 + - + -
79A PHE* 3.8 29.6 - - + -
146A LEU* 3.8 15.3 - - + -
147A TYR* 3.4 34.1 - - - +
148A VAL* 4.1 4.9 - - + +
152A VAL* 1.3 75.6 - - - +
154A LYS* 1.3 64.3 + - - +
176A THR* 3.6 3.1 - - - +
177A TYR* 2.7 42.6 + - + +
186A PRO* 3.9 24.2 - - + -
189A HIS* 4.6 2.2 - - + -
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.2 9.9 - - - +
147A TYR* 2.9 63.5 + - + +
149A ARG* 3.8 40.9 - - + +
150A ASP* 5.0 4.9 + - - -
152A VAL* 4.8 5.2 - - + -
153A LEU* 1.3 75.6 - - - +
155A GLY* 1.3 59.6 + - - +
156A ASP* 4.9 1.6 - - - +
175A THR 3.3 4.5 - - - +
176A THR* 3.2 38.9 + - + +
177A TYR* 4.2 4.0 - - - -
97C ASP 6.0 0.4 + - - -
124C ASN* 4.8 13.1 + - - +
126C PRO* 5.7 6.9 - - - +
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLU* 3.5 22.7 - - - -
145A LYS 3.3 6.5 - - - -
146A LEU* 4.3 0.9 - - - -
154A LYS* 1.3 76.0 - - - +
156A ASP* 1.3 66.3 + - - +
157A VAL* 5.8 0.2 - - - -
173A PHE* 3.9 1.4 - - - +
174A LYS* 3.6 1.6 - - - -
175A THR* 2.8 43.1 + - - -
177A TYR* 4.0 5.6 - - - -
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLU* 4.2 0.9 - - - +
145A LYS* 2.8 39.8 + - + +
147A TYR* 3.0 22.6 + - + -
154A LYS* 4.9 1.6 - - - +
155A GLY* 1.3 80.4 + - - +
157A VAL* 1.3 61.7 + - - +
173A PHE 3.4 4.9 - - - +
174A LYS* 4.0 19.9 - - - +
175A THR 4.6 0.7 + - - -
158B ASN* 3.9 26.5 + - + +
170B ARG* 2.9 36.1 + - - +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A KZ4 3.6 21.3 - - + -
142A SER* 4.0 17.9 - - - -
143A THR 3.4 26.9 - - - +
144A GLU* 3.8 18.6 - - + -
145A LYS* 5.8 1.1 - - - -
155A GLY 5.8 0.2 - - - -
156A ASP* 1.3 77.3 - - - +
158A ASN* 1.3 77.8 + - - +
159A THR* 3.8 3.7 + - + -
171A CYS 3.9 0.3 - - - +
172A ASP* 3.7 0.2 - - - -
173A PHE* 2.8 56.3 + - + +
145B LYS* 4.6 2.9 - - - +
158B ASN* 5.3 2.0 - - - -
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Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL* 1.3 80.7 + - - +
159A THR* 1.3 57.5 + - - +
170A ARG* 2.0 47.5 + - - +
171A CYS 3.6 0.7 - - - -
172A ASP* 3.2 25.0 + - - +
173A PHE 4.8 1.2 + - - +
145B LYS* 3.6 31.0 - - - +
156B ASP* 4.8 0.7 - - + -
157B VAL* 3.7 1.3 - - - -
158B ASN* 3.3 46.3 + - - +
172B ASP* 3.5 16.5 + - - +
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A KZ4 4.0 14.8 + - + +
139A TRP* 3.7 24.7 - - + -
140A GLU 4.1 7.6 + - - -
141A PRO 4.5 2.8 + - - -
142A SER* 3.9 25.4 - - - -
157A VAL* 4.3 2.9 - - - +
158A ASN* 1.3 73.8 - - - +
160A ALA* 1.3 76.0 + - - +
170A ARG* 3.2 13.2 - - - -
171A CYS 2.9 30.5 + - - +
173A PHE* 3.9 16.4 - - + -
145B LYS* 5.5 0.4 - - - -
188B TYR* 4.2 8.3 + - - -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TRP* 3.4 12.3 - - - -
140A GLU* 3.1 26.0 + - - +
159A THR* 1.3 86.3 + - - +
161A LEU* 1.3 60.2 + - - +
168A HIS* 4.0 16.8 - - + -
169A TYR 3.2 13.9 - - - +
170A ARG* 4.2 7.6 - - - +
147B TYR* 6.0 1.3 - - + -
188B TYR* 3.9 28.7 + - + +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASP* 3.5 31.0 - - + +
56A ILE* 4.9 5.2 - - + -
95A TYR* 4.1 10.1 - - + +
136A THR* 4.0 23.3 - - + -
138A LYS 3.4 18.2 - - - +
139A TRP* 3.5 44.4 - - + +
160A ALA* 1.3 73.4 - - - +
162A SER* 1.3 64.4 + - - +
168A HIS* 3.3 5.8 - - - -
169A TYR* 2.7 57.4 + - + +
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Residues in contact with SER 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 3.6 4.2 - - - -
137A VAL* 2.8 46.2 + - - +
138A LYS* 2.8 24.7 + - - +
140A GLU* 3.8 21.9 - - - +
160A ALA 4.1 0.6 + - - -
161A LEU* 1.3 73.9 - - - +
163A LEU* 1.3 62.1 + - - +
167A GLY 3.8 6.3 - - - -
168A HIS* 3.8 9.0 - - - -
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PRO* 3.9 20.2 - - + -
135A ARG* 3.5 27.8 - - - +
136A THR* 4.2 8.5 - - + -
137A VAL* 3.6 6.0 - - - +
161A LEU 4.3 0.7 - - - +
162A SER* 1.3 81.7 - - - +
164A GLU* 1.3 58.0 + - - +
165A GLY 3.1 4.3 - - - +
166A GLY* 2.9 39.9 + - - +
167A GLY 3.0 12.2 + - - +
168A HIS 4.2 10.5 - - - +
169A TYR* 3.7 34.5 - - + +
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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