Contacts of the strand formed by residues 137 - 145 (chain A) in PDB entry 1NQG
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ARG* 4.1 5.4 + - - -
135A GLU 4.9 0.2 - - - -
136A PRO* 1.3 77.5 - - - +
138A THR* 1.3 64.8 + - - -
139A GLU* 5.8 0.2 - - - -
156A THR* 3.1 1.6 - - - -
157A GLN 2.7 41.1 + - - -
158A GLN* 4.6 3.7 + - - -
593A THR* 5.8 3.1 - - - -
594A PHE 4.5 11.4 - - - -
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Residues in contact with THR 138 (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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133A ARG* 5.7 0.2 - - - +
137A GLY* 1.3 76.2 - - - -
139A GLU* 1.3 61.3 + - - +
140A ILE* 5.4 0.5 - - - +
154A VAL* 6.1 1.8 - - - -
155A SER 2.9 13.5 - - - -
156A THR* 3.2 20.4 - - - +
158A GLN* 4.1 13.5 - - - +
593A THR* 3.8 2.8 - - - +
594A PHE* 2.8 59.3 + - + -
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Residues in contact with GLU 139 (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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31A ARG* 6.0 0.3 + - - -
35A ASP* 4.9 8.1 - - - +
133A ARG* 4.6 14.8 + - - +
135A GLU* 6.1 0.3 - - - +
138A THR* 1.3 76.2 + - - +
140A ILE* 1.3 67.3 + - - +
141A SER* 4.0 16.6 + - - +
153A ASP 4.0 0.7 - - - +
154A VAL* 3.6 2.4 - - - +
155A SER* 2.8 44.4 + - - +
562A ARG* 5.8 0.9 + - - -
591A SER* 4.1 12.9 + - - -
592A TYR 3.5 11.2 - - - +
593A THR* 4.1 21.3 + - + +
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Residues in contact with ILE 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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138A THR* 5.4 0.4 - - - +
139A GLU* 1.3 75.6 - - - +
141A SER* 1.3 71.0 + - - +
153A ASP 3.6 7.0 - - - +
154A VAL* 4.3 21.1 - - + -
591A SER* 3.4 0.9 - - - -
592A TYR* 2.8 43.0 + - + +
594A PHE* 4.3 22.9 - - + -
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Residues in contact with SER 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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139A GLU* 4.0 13.8 + - - +
140A ILE* 1.3 85.5 - - - +
142A ALA* 1.3 68.9 + - - +
151A ASN* 4.4 1.6 - - - -
152A TYR* 3.9 0.7 - - - +
153A ASP* 2.9 41.3 + - - +
590A GLY 3.2 16.8 - - - -
591A SER* 3.8 13.2 - - - +
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Residues in contact with ALA 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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141A SER* 1.3 81.7 - - - +
143A GLY* 1.3 56.5 + - - +
144A TRP* 4.8 14.5 - - + -
151A ASN* 2.2 37.0 - - - +
152A TYR* 3.0 15.7 - - + -
589A SER* 3.7 3.9 + - - -
590A GLY 3.1 26.8 + - - +
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Residues in contact with GLY 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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142A ALA* 1.3 75.1 - - - +
144A TRP* 1.3 75.5 + - - -
149A TYR* 4.3 11.0 - - - -
150A GLN* 3.5 5.4 - - - +
151A ASN* 2.6 37.6 + - - +
587A THR* 5.4 0.2 - - - -
588A LEU 3.4 10.5 - - - -
589A SER* 4.1 6.1 - - - -
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Residues in contact with TRP 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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142A ALA* 4.8 12.6 - - + -
143A GLY* 1.3 87.8 - - - -
145A GLY* 1.3 58.5 + - - +
149A TYR* 3.6 10.0 - - - -
150A GLN* 4.2 25.6 + - + +
151A ASN 5.9 0.4 - - - -
587A THR* 3.3 4.2 - - - +
588A LEU* 2.9 60.5 + - + +
589A SER* 5.5 1.8 - - - -
590A GLY 5.7 1.1 - - - -
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Residues in contact with GLY 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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144A TRP* 1.3 78.2 - - - +
146A SER* 1.3 53.4 + - - -
147A ASN 2.8 17.5 + - - -
148A SER* 3.2 5.9 + - - -
149A TYR* 3.1 36.1 + - - -
586A TYR* 3.4 10.5 - - - -
587A THR* 4.3 0.9 - - - -
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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