Contacts of the strand formed by residues 120 - 132 (chain B) in PDB entry 2NQY
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 GLY 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ILE 3.9 0.7 - - - +
116B THR* 3.3 7.6 - - - +
117B VAL 3.0 31.1 + - - +
118B ASP 3.2 1.6 - - - -
119B GLY* 1.3 78.8 - - - +
121B THR* 1.3 62.0 + - - -
122B TYR* 4.2 3.3 - - - -
148B ARG* 3.5 19.5 - - - -
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Residues in contact with THR 121 (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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114B THR* 4.0 20.9 - - - +
115B ILE 3.5 3.4 - - - +
116B THR* 3.2 26.0 + - - +
120B GLY* 1.3 73.7 - - - -
122B TYR* 1.3 60.1 + - - +
148B ARG* 3.5 2.6 - - - +
149B ARG* 2.8 70.5 + - - +
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Residues in contact with TYR 122 (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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97B ILE* 3.9 7.4 - - + -
98B VAL 3.7 5.4 - - - -
99B ASP* 2.5 31.5 + - - -
114B THR* 3.1 9.1 - - - -
115B ILE* 2.8 53.8 + - + +
117B VAL* 3.7 23.8 - - + -
118B ASP* 4.5 2.9 + - - +
120B GLY 4.2 2.5 - - - -
121B THR* 1.3 78.0 - - - +
123B ASP* 1.3 62.0 + - - +
124B ILE 3.8 0.2 + - - -
146B SER* 3.8 7.4 - - - -
147B THR 3.2 17.5 - - - +
148B ARG* 2.8 56.5 + - + -
152B ARG* 3.6 5.4 + - - -
157B ILE* 4.7 3.5 - - - +
162B HIS* 3.6 27.5 + + - -
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Residues in contact with ASP 123 (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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105B ARG* 2.9 27.2 + - - +
111B PRO* 3.9 18.9 - - + +
113B GLY 3.6 2.9 - - - -
114B THR* 3.5 7.4 - - - +
121B THR 4.3 0.2 - - - -
122B TYR* 1.3 72.9 - - - +
124B ILE* 1.3 59.8 + - - +
125B TYR* 3.3 33.3 - - + +
146B SER* 3.4 3.1 - - - -
147B THR 2.9 30.3 + - - -
149B ARG* 3.1 37.7 + - - +
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Residues in contact with ILE 124 (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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111B PRO* 3.2 4.7 - - - +
112B LYS* 2.6 33.6 + - + -
113B GLY 2.9 13.7 + - - +
114B THR 3.9 24.5 - - - +
115B ILE* 3.9 13.2 - - + -
122B TYR 4.2 4.7 - - - +
123B ASP* 1.3 76.7 - - - +
125B TYR* 1.3 60.9 + - - +
145B TRP 3.2 9.6 - - - +
146B SER* 3.8 14.6 - - - +
165B ALA* 4.2 14.6 - - + -
166B TRP* 3.6 19.3 - - + -
169B LEU* 3.8 24.7 - - + -
171B MET* 3.6 21.5 - - + -
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Residues in contact with TYR 125 (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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105B ARG* 3.4 19.6 + - - -
106B PRO 4.5 1.8 + - - -
107B PRO* 3.5 42.2 - - + -
109B ALA* 3.1 37.2 - - + -
110B THR 3.7 13.0 - - - +
111B PRO* 3.7 16.8 - - + +
112B LYS* 4.3 4.3 - - - -
123B ASP* 3.3 43.2 - - + +
124B ILE* 1.3 74.9 - - - +
126B GLU* 1.3 61.2 + - - +
144B TYR* 3.6 0.2 - - - -
145B TRP* 2.9 41.2 + - + -
147B THR* 3.9 12.1 - - - -
171B MET* 3.3 11.2 - - - +
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Residues in contact with GLU 126 (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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109B ALA* 4.7 5.0 - - - +
110B THR 5.2 1.7 + - - +
112B LYS* 3.7 30.8 + - + +
125B TYR* 1.3 75.3 - - - +
127B THR* 1.3 75.5 + - - +
142B SER* 4.3 9.7 + - - -
143B GLN 3.3 11.9 - - - +
144B TYR* 3.3 28.6 + - + -
170B GLY 5.1 1.6 - - - +
171B MET* 3.8 17.0 - - + +
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Residues in contact with THR 127 (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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107B PRO* 4.2 14.6 - - + +
109B ALA* 3.9 23.8 - - + -
126B GLU* 1.3 82.5 - - - +
128B ASP* 1.3 61.5 + - - +
142B SER* 3.4 8.0 + - - -
143B GLN* 2.7 55.9 + - - +
145B TRP* 3.1 19.2 + - - +
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Residues in contact with ASP 128 (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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127B THR* 1.3 79.1 - - - +
129B ARG* 1.3 75.9 + - - +
130B THR* 3.8 18.0 + - - -
140B THR* 4.1 10.5 - - - +
141B PHE 3.5 13.1 - - - +
142B SER* 4.5 5.6 + - - +
143B GLN* 5.0 0.2 - - - +
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Residues in contact with ARG 129 (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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128B ASP* 1.3 76.6 - - - +
130B THR* 1.3 61.0 + - - +
131B ASN 4.0 0.2 - - - -
132B GLN* 3.3 44.8 + - + +
133B PRO* 4.6 1.2 - - - +
139B ALA 4.6 0.2 - - - -
140B THR* 3.2 7.9 - - - +
141B PHE* 2.9 62.9 + - + +
143B GLN* 3.5 35.7 - - + +
3002B XYP 2.9 33.2 + - - -
1D XYP 3.3 19.2 + - - -
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Residues in contact with THR 130 (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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31A ASN* 3.8 27.3 + - + +
32A SER 5.9 0.2 - - - +
128B ASP* 3.8 17.0 + - - -
129B ARG* 1.3 72.9 - - - +
131B ASN* 1.3 84.5 + - - +
132B GLN* 3.3 17.5 + - - +
140B THR* 3.6 13.0 - - + +
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Residues in contact with ASN 131 (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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31A ASN* 3.9 12.3 + - - +
35A THR* 4.0 18.0 + - - +
193A ASN* 2.7 35.9 + - - +
194A VAL 4.6 0.8 + - - -
195A TYR* 3.8 22.3 + - + +
130B THR* 1.3 86.2 - - + +
132B GLN* 1.3 63.1 + - - +
133B PRO* 4.7 0.7 - - - +
138B VAL* 3.4 21.3 - - + +
139B ALA 3.2 8.4 + - - -
140B THR* 3.1 13.8 + - - -
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Residues in contact with GLN 132 (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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129B ARG* 3.3 48.3 + - + +
130B THR 3.4 28.4 + - - +
131B ASN* 1.3 80.4 + - - +
133B PRO* 1.3 85.5 - - + +
137B GLY 3.4 0.2 - - - +
138B VAL* 3.3 5.4 - - - -
139B ALA* 2.8 29.0 + - - +
141B PHE* 4.1 8.9 - - + -
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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