Contacts of the strand formed by residues 103 - 111 (chain A) in PDB entry 2NSQ
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 ASP 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LYS* 4.8 15.3 - - + +
94A PHE* 3.2 4.7 - - - -
95A ASP* 2.8 52.7 + - + +
97A ASN* 3.5 15.9 + - - +
100A THR* 5.2 0.9 + - - -
101A ARG 3.4 3.7 + - - +
102A ASP* 1.3 71.0 - - - +
104A PHE* 1.3 70.3 + - - +
105A LEU* 3.5 6.3 + - + +
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Residues in contact with PHE 104 (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 GLU* 4.1 9.2 - - + -
93A VAL 4.1 2.9 - - - -
94A PHE* 3.6 24.2 - + + -
102A ASP 3.8 1.4 + - - -
103A ASP* 1.3 78.3 + - - +
105A LEU* 1.3 65.1 + - - +
106A GLY* 3.3 43.5 - - - -
107A GLN* 3.6 15.0 - - + -
134A ARG 4.3 0.2 - - - -
135A PRO* 4.2 3.6 - - + -
136A ARG* 3.5 73.8 - - + +
140A SER* 5.9 0.2 - - - -
142A VAL* 4.4 6.1 - - + +
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Residues in contact with LEU 105 (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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32A LEU* 4.3 21.2 - - + +
33A ALA* 3.9 34.1 + - + +
35A LYS* 4.4 19.1 - - + -
41A SER* 4.5 8.7 - - - +
43A PRO* 4.8 2.0 - - + -
93A VAL* 2.7 39.3 + - + +
94A PHE 4.3 1.3 - - - +
95A ASP* 4.0 26.7 - - + +
103A ASP* 3.8 12.6 - - + +
104A PHE* 1.3 80.5 - - - +
106A GLY* 1.3 56.5 + - - +
133A LEU* 4.5 8.5 - - - +
142A VAL* 3.4 22.7 - - - +
143A LYS 4.6 2.9 + - - +
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Residues in contact with GLY 106 (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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93A VAL* 2.8 27.4 + - - +
104A PHE* 3.3 25.9 - - - -
105A LEU* 1.3 80.5 - - - +
107A GLN* 1.3 58.3 + - - -
133A LEU* 3.8 12.0 - - - +
134A ARG 3.5 7.2 - - - -
142A VAL* 3.9 9.2 - - - -
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Residues in contact with GLN 107 (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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90A LEU* 3.9 24.6 - - + +
91A PHE 3.1 12.8 - - - +
92A GLU* 4.2 6.5 - - + +
104A PHE* 3.8 9.7 - - + -
106A GLY* 1.3 74.6 - - - +
108A VAL* 1.3 70.8 + - - +
109A ASP* 5.0 8.1 + - - +
133A LEU* 3.8 1.7 - - - +
134A ARG* 2.8 50.0 + - + +
135A PRO 3.9 14.5 + - - +
136A ARG* 3.9 24.5 + - - +
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Residues in contact with VAL 108 (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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90A LEU* 3.6 2.8 - - - +
91A PHE* 2.8 46.6 + - + +
107A GLN* 1.3 80.2 - - - +
109A ASP* 1.3 67.0 + - - +
110A VAL* 4.9 3.6 - - + +
131A PHE* 3.6 48.5 - - + +
132A LEU 3.9 10.1 - - - +
133A LEU* 3.8 18.2 - - + -
134A ARG* 5.1 3.1 - - - -
146A LEU* 4.1 12.6 - - + -
148A LEU* 4.7 6.7 - - + -
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Residues in contact with ASP 109 (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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50A TYR* 2.6 30.9 + - - -
88A ARG* 2.7 49.7 + - - +
89A LEU 3.7 2.2 - - - -
90A LEU* 3.5 19.7 - - + +
107A GLN* 4.3 9.6 + - - +
108A VAL* 1.3 77.8 - - - +
110A VAL* 1.3 58.1 + - - +
111A PRO* 3.9 3.1 - - - +
134A ARG* 5.8 1.6 - - - +
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Residues in contact with VAL 110 (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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88A ARG* 3.4 6.6 - - - +
89A LEU* 2.8 65.4 + - + +
91A PHE* 3.7 15.0 - - + -
108A VAL* 4.0 7.4 - - + -
109A ASP* 1.3 73.0 + - - +
111A PRO* 1.3 83.0 - - + +
112A LEU* 3.8 7.5 + - + +
115A LEU* 4.4 9.0 - - + -
131A PHE* 5.0 9.0 - - + -
150A MET* 3.9 27.4 - - + -
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Residues in contact with PRO 111 (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 HIS 4.6 0.2 - - - +
88A ARG* 3.6 38.8 - - + +
109A ASP 3.9 2.9 - - - +
110A VAL* 1.3 102.6 - - + +
112A LEU* 1.3 62.4 + - - +
113A SER* 3.5 13.0 + - - +
114A HIS* 4.9 1.9 + - + +
115A LEU* 4.1 7.4 - - - +
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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