Contacts of the strand formed by residues 139 - 148 (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 ALA 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASN* 5.9 1.3 - - - +
193A ASN* 4.2 7.4 - - - +
92B LEU* 3.9 18.6 - - + -
129B ARG 4.0 0.3 - - - +
131B ASN* 3.2 4.1 + - - -
132B GLN 2.8 29.8 + - - +
134B SER* 3.4 22.9 - - - +
136B LYS* 4.6 5.6 - - + +
137B GLY 3.7 0.9 - - - +
138B VAL* 1.3 78.1 - - - +
140B THR* 1.3 63.2 + - - +
141B PHE* 3.5 8.7 - - + -
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Residues in contact with THR 140 (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* 4.8 4.8 + - - +
37A SER* 6.6 0.2 - - - -
193A ASN* 4.5 7.3 + - - +
92B LEU* 4.3 8.7 - - - +
128B ASP* 4.1 14.4 - - - +
129B ARG 3.2 14.8 - - - +
130B THR* 3.6 15.5 - - + +
131B ASN* 3.1 24.9 + - - -
139B ALA* 1.3 72.4 - - - +
141B PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 141 (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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87B TRP* 3.6 22.0 - + - -
92B LEU* 3.2 29.8 - - + +
94B GLU* 3.6 19.7 - - + -
128B ASP* 3.5 5.5 - - - +
129B ARG* 2.9 63.3 + - + +
132B GLN* 4.1 3.1 - - + -
133B PRO 3.6 25.8 - - - -
134B SER* 3.7 14.6 - - - -
139B ALA 3.5 22.0 - - - -
140B THR* 1.3 76.2 - - - +
142B SER* 1.3 72.1 + - - +
143B GLN* 4.2 0.7 - - + -
1D XYP 3.9 8.1 - - - -
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Residues in contact with SER 142 (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 LEU 3.6 4.4 + - - -
93B VAL* 3.4 10.5 - - - -
94B GLU 3.0 23.4 + - - -
126B GLU* 4.3 10.2 + - - -
127B THR 3.4 10.0 + - - -
128B ASP* 4.5 6.0 + - - +
141B PHE* 1.3 79.6 - - - +
143B GLN* 1.3 61.9 + - - +
144B TYR* 3.8 27.0 + - - -
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Residues in contact with GLN 143 (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 GLU* 2.7 39.7 + - - +
96B TYR* 3.9 6.6 - - + -
126B GLU* 3.3 7.1 - - - -
127B THR* 2.7 57.6 + - - +
129B ARG* 3.5 29.6 - - + +
141B PHE* 4.2 1.8 - - + -
142B SER* 1.3 76.8 - - - +
144B TYR* 1.3 66.7 + - - +
145B TRP* 3.4 19.7 - - + +
3002B XYP 3.2 28.1 + - - +
1D XYP 3.5 2.8 + - - -
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Residues in contact with TYR 144 (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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91B PRO* 4.8 1.7 - - - +
93B VAL* 3.6 28.0 - - + +
94B GLU 3.1 5.9 + - - +
95B TYR* 3.2 3.9 - - + +
96B TYR* 2.8 32.7 + - - +
125B TYR 3.6 2.9 - - - -
126B GLU* 3.3 27.4 + - + -
142B SER* 3.8 14.2 - - - -
143B GLN* 1.3 80.9 - - - +
145B TRP* 1.3 58.5 + - - +
166B TRP* 3.8 33.0 - + + -
171B MET* 3.4 41.5 - - + -
172B ASN* 2.7 37.2 + - - -
173B MET* 3.8 8.5 - - + -
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Residues in contact with TRP 145 (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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81B TYR* 4.0 5.8 - + - -
96B TYR* 3.3 58.8 - + + -
98B VAL* 4.1 9.4 - - + -
106B PRO* 3.7 26.5 - - + -
107B PRO* 3.6 31.4 - - + +
123B ASP 4.2 0.2 - - - -
124B ILE* 3.2 12.1 - - - +
125B TYR* 2.9 56.0 + - + +
127B THR* 3.1 21.7 + - + -
143B GLN* 3.4 25.9 - - - +
144B TYR* 1.3 78.8 - - - +
146B SER* 1.3 59.0 + - - +
147B THR* 4.2 5.2 - - - +
166B TRP* 3.7 3.7 + - - -
171B MET* 4.4 0.2 - - - +
3002B XYP 3.7 27.6 - - - -
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Residues in contact with SER 146 (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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96B TYR 2.9 11.1 + - - +
97B ILE* 3.3 3.2 - - - -
98B VAL* 2.7 33.4 + - - +
115B ILE* 4.0 1.7 - - - +
122B TYR* 3.8 7.5 - - - -
123B ASP 3.4 5.4 - - - -
124B ILE* 3.8 11.1 - - - +
145B TRP* 1.3 70.4 + - - +
147B THR* 1.3 57.8 + - - +
162B HIS* 2.9 39.9 + - - -
166B TRP* 3.0 21.8 + - - -
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Residues in contact with THR 147 (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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98B VAL* 3.7 15.7 - - + +
101B TRP* 4.2 6.7 - - + -
105B ARG* 2.8 52.1 + - + +
106B PRO* 3.4 35.7 + - + +
122B TYR* 3.6 3.7 - - - -
123B ASP 2.9 22.5 + - - -
125B TYR* 3.9 13.6 - - - -
145B TRP* 4.2 9.7 - - - +
146B SER* 1.3 75.2 + - - +
148B ARG* 1.3 65.0 + - - +
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Residues in contact with ARG 148 (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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98B VAL 2.9 19.0 + - - +
99B ASP* 3.5 24.7 - - - +
101B TRP* 3.2 13.1 - - + -
105B ARG* 3.1 15.4 + - - -
117B VAL 3.9 1.2 + - - -
118B ASP* 2.8 30.7 + - - +
119B GLY* 3.3 18.8 + - - -
120B GLY* 3.5 7.2 - - - -
121B THR 3.5 12.8 - - - +
122B TYR* 2.8 49.0 + - + -
147B THR* 1.3 75.5 - - - +
149B ARG* 1.3 62.7 + - - +
150B SER* 3.3 27.9 + - - +
152B ARG* 3.3 36.1 - - - +
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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