Contacts of the strand formed by residues 139 - 148 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.8 19.5 - - + -
129A ARG 4.0 0.7 - - - +
131A ASN* 3.1 7.1 + - - +
132A GLN 2.8 30.1 + - - +
134A SER* 3.5 23.3 - - - +
136A LYS* 4.7 4.9 - - + +
137A GLY 3.6 0.7 - - - +
138A VAL* 1.3 77.4 - - - +
140A THR* 1.3 62.4 + - - +
141A PHE* 3.5 8.6 - - + -
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Residues in contact with THR 140 (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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92A LEU* 4.6 5.4 - - - +
128A ASP* 4.1 13.0 - - - +
129A ARG 3.2 12.8 - - - +
130A THR* 3.5 15.0 - - + +
131A ASN* 3.1 26.2 + - - -
139A ALA* 1.3 73.8 - - - +
141A PHE* 1.3 66.3 + - - +
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Residues in contact with PHE 141 (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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87A TRP* 3.6 26.7 - + - -
92A LEU* 3.4 29.8 - - + +
94A GLU* 3.7 16.2 - - + -
128A ASP* 3.5 5.2 - - - +
129A ARG* 2.9 61.6 + - + +
132A GLN* 4.1 3.1 - - + -
133A PRO 3.5 26.0 - - - -
134A SER* 3.7 15.0 - - - -
139A ALA* 3.5 24.5 - - + -
140A THR* 1.3 76.9 - - - +
142A SER* 1.3 71.5 + - - +
143A GLN* 4.2 1.1 - - + -
1C XYP 4.0 9.0 - - - -
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Residues in contact with SER 142 (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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92A LEU 3.7 4.4 + - - -
93A VAL* 3.5 9.8 - - - -
94A GLU 3.0 23.7 + - - -
126A GLU* 4.0 12.5 + - - -
127A THR 3.3 10.3 + - - -
128A ASP* 4.6 6.1 + - - -
141A PHE* 1.3 79.6 - - - +
143A GLN* 1.3 61.3 - - - +
144A TYR* 3.7 26.9 + - - -
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Residues in contact with GLN 143 (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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94A GLU* 2.7 39.1 + - + +
96A TYR* 3.9 13.6 + - + -
126A GLU* 3.3 6.8 - - - -
127A THR* 2.7 56.8 + - - +
129A ARG* 3.6 26.0 - - + +
141A PHE* 4.2 1.8 - - + -
142A SER* 1.3 76.7 - - - +
144A TYR* 1.3 65.4 + - - +
145A TRP* 3.4 19.6 - - + +
3001A XYP 3.9 18.2 + - - -
1C XYP 3.3 12.3 + - - -
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Residues in contact with TYR 144 (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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91A PRO* 4.8 1.7 - - - +
93A VAL* 3.6 28.0 - - + +
94A GLU 3.0 6.3 + - - +
95A TYR* 3.3 3.8 - - + -
96A TYR* 2.8 29.4 + - - +
125A TYR 3.6 3.4 - - - -
126A GLU* 3.3 24.8 + - + -
142A SER* 3.7 15.8 + - - -
143A GLN* 1.3 80.6 - - - +
145A TRP* 1.3 62.0 + - - +
166A TRP* 3.9 31.4 - + + -
171A MET* 3.4 44.4 - - + -
172A ASN* 2.7 38.6 + - - -
173A MET* 3.8 7.0 - - + -
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Residues in contact with TRP 145 (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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81A TYR* 4.1 15.5 - + - -
96A TYR* 3.4 60.6 - + + -
98A VAL* 4.1 9.9 - - + -
106A PRO* 3.8 27.6 - - + -
107A PRO* 3.6 26.5 - - + +
123A ASP 4.2 0.2 - - - -
124A ILE* 3.2 12.3 - - - +
125A TYR* 2.9 53.6 + - + +
127A THR* 3.2 20.2 + - - -
143A GLN* 3.4 27.7 - - - +
144A TYR* 1.3 78.1 - - - +
146A SER* 1.3 59.7 + - - +
147A THR* 4.2 7.0 - - - +
166A TRP* 4.0 3.4 - - - -
171A MET* 4.3 0.4 - - - +
3001A XYP 4.1 17.0 - - - -
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Residues in contact with SER 146 (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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96A TYR 2.9 11.4 + - - +
97A ILE* 3.4 3.5 - - - -
98A VAL* 2.8 29.3 + - - +
115A ILE* 4.0 1.4 - - - +
122A TYR* 3.9 10.4 - - - -
123A ASP 3.4 4.5 - - - -
124A ILE* 3.8 9.4 - - - +
145A TRP* 1.3 69.3 - - - +
147A THR* 1.3 63.8 + - - +
162A HIS* 2.9 39.4 + - - -
166A TRP* 3.0 22.8 + - - -
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Residues in contact with THR 147 (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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98A VAL* 3.7 15.7 - - + +
101A TRP* 4.2 7.2 - - + -
105A ARG* 2.9 48.1 + - + +
106A PRO* 3.4 34.6 + - + +
122A TYR* 3.5 3.1 - - - -
123A ASP 2.9 23.4 + - - -
125A TYR* 4.0 15.9 - - - -
145A TRP* 4.2 10.4 - - - +
146A SER* 1.3 77.5 + - - +
148A ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 148 (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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98A VAL 3.0 16.1 + - - +
99A ASP* 3.7 19.3 - - - +
101A TRP* 3.2 11.0 - - + -
105A ARG* 3.1 19.2 + - - -
117A VAL 3.9 1.2 + - - -
118A ASP* 2.9 29.5 + - - +
119A GLY* 3.3 19.2 + - - -
120A GLY* 3.5 8.2 - - - -
121A THR 3.6 9.4 - - - +
122A TYR* 2.7 60.1 + - + -
147A THR* 1.3 72.1 - - - +
149A ARG* 1.3 63.4 + - - +
150A SER* 3.3 26.6 + - - +
152A ARG* 3.3 36.6 - - - +
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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