Contacts of the strand formed by residues 111 - 122 (chain V) in PDB entry 4N3E
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 111 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12V SER 3.8 1.3 - - - -
13V PRO* 3.4 24.9 - - - -
14V ILE 4.0 2.6 - - - +
16V PRO* 4.2 5.4 - - - +
107V ALA* 4.0 5.0 - - - +
108V VAL 2.8 24.0 + - - +
109V GLY 4.5 0.2 - - - +
110V GLY* 1.3 83.5 - - - +
112V SER* 1.3 61.8 + - - -
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Residues in contact with SER 112 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V GLU* 3.7 6.6 - - - +
12V SER* 2.3 56.4 + - - -
14V ILE 3.1 18.9 + - - -
16V PRO* 4.6 11.9 - - - -
19V LEU* 4.1 7.8 - - - +
105V LEU* 5.6 4.0 - - - -
106V GLU 3.8 11.0 - - - -
108V VAL* 3.6 12.6 + - - +
111V GLY* 1.3 71.2 - - - -
113V LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V GLU* 6.5 1.3 - - + -
10V GLU 3.4 9.6 - - - +
11V GLU* 4.9 11.0 - - + -
104V LYS 3.8 0.7 - - - +
105V LEU* 3.4 10.8 - - - +
106V GLU* 2.9 61.1 + - + +
108V VAL* 3.2 35.4 - - + +
112V SER* 1.3 77.6 - - - +
114V GLY* 1.3 67.9 + - - +
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Residues in contact with GLY 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V GLU* 3.4 7.3 - - - +
10V GLU* 2.8 34.3 + - - +
104V LYS 3.6 6.3 - - - -
105V LEU* 4.2 11.6 - - - +
113V LYS* 1.3 83.1 - - - +
115V LYS* 1.3 62.2 + - - +
116V ILE* 4.1 10.3 - - - -
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Residues in contact with LYS 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83U LYS* 3.9 22.8 - - - +
7V VAL* 3.9 27.1 - - + +
8V LYS 3.3 13.2 - - - +
9V GLU* 3.9 24.2 - - + -
102V GLU 3.7 1.8 - - - +
104V LYS* 3.2 38.8 + - + +
114V GLY* 1.3 72.1 - - - +
116V ILE* 1.3 63.4 + - - +
117V THR* 4.9 9.4 - - + +
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Residues in contact with ILE 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6V ILE 4.0 0.5 - - - +
7V VAL* 3.7 0.3 - - - +
8V LYS* 2.9 38.8 + - + +
10V GLU* 5.5 9.2 - - + +
101V TYR* 5.6 3.8 - - + -
102V GLU 3.1 11.9 - - - +
103V VAL* 4.3 24.0 - - + -
105V LEU* 5.4 4.0 - - + -
114V GLY* 4.5 15.3 - - - -
115V LYS* 1.3 79.9 - - - +
117V THR* 1.3 68.9 + - - +
118V VAL* 3.8 24.2 - - + -
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Residues in contact with THR 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V THR* 4.5 5.0 - - - +
6V ILE 3.2 9.2 - - - -
7V VAL* 3.9 28.9 - - + -
100V VAL 3.7 1.4 + - - +
101V TYR* 3.5 1.4 - - - -
102V GLU* 2.6 63.8 + - + +
115V LYS* 4.9 11.7 - - + +
116V ILE* 1.3 79.0 - - - +
118V VAL* 1.3 64.0 + - - +
119V THR* 4.5 8.3 + - - -
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Residues in contact with VAL 118 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V TYR 3.9 0.7 - - - +
5V THR* 3.2 3.5 - - - +
6V ILE* 2.9 31.5 + - - +
99V VAL* 3.5 26.2 - - + -
100V VAL 3.3 3.1 - - - +
101V TYR* 3.8 26.0 - - + -
116V ILE* 3.8 18.2 - - + -
117V THR* 1.3 78.6 - - - +
119V THR* 1.3 67.3 + - - +
120V TYR* 3.7 16.8 - - + +
137V GLU* 3.6 30.7 - - - +
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Residues in contact with THR 119 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U THR* 5.5 3.6 - - + +
7U VAL* 5.7 5.6 - - + -
3V ALA* 4.0 10.8 - - + -
4V TYR 3.4 2.2 - - - -
5V THR* 2.4 27.8 + - - +
99V VAL* 3.2 6.8 - - - +
100V VAL* 2.9 45.8 + - + +
117V THR* 4.5 5.7 + - - -
118V VAL* 1.3 74.1 + - - +
120V TYR* 1.3 63.3 + - - +
121V HIS* 3.7 30.8 + - + +
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Residues in contact with TYR 120 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V ALA* 3.0 18.4 - - - +
4V TYR* 2.7 34.5 + - + +
6V ILE* 5.5 1.3 - - + -
96V ILE* 4.6 8.3 - - + -
98V LYS 4.1 1.6 - - - -
99V VAL* 4.0 23.7 - - + +
101V TYR* 5.4 2.9 + - - -
118V VAL* 3.7 26.2 - - + +
119V THR* 1.3 76.0 - - - +
121V HIS* 1.3 60.1 + - - +
122V PRO* 3.5 5.1 - - - +
128V VAL* 4.0 19.6 - - + +
132V GLU* 3.4 39.0 + - + -
133V VAL* 4.0 32.6 - - + -
136V GLY* 3.7 21.1 + - - -
137V GLU* 3.9 7.8 + - - -
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Residues in contact with HIS 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U VAL* 4.9 23.9 + - + +
1V MET 4.2 17.8 + - - -
3V ALA* 4.0 12.3 - - + +
96V ILE* 3.8 3.9 - - - +
97V GLU* 2.8 32.5 + - + +
98V LYS* 2.8 56.4 + - + +
100V VAL* 4.6 6.2 - - + +
119V THR* 3.7 32.0 + - + +
120V TYR* 1.3 70.8 - - - +
122V PRO* 1.3 67.2 - - + +
128V VAL* 4.1 2.0 - - - -
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Residues in contact with PRO 122 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1V MET 5.1 0.7 - - - +
2V ALA 4.2 20.4 - - - +
3V ALA* 4.0 14.4 - - + +
95V ASN 3.8 3.1 - - - +
97V GLU* 3.7 6.1 - - - +
120V TYR 3.5 9.0 - - - +
121V HIS* 1.3 90.9 - - + +
123V LYS* 1.3 68.6 + - - +
124V PRO* 4.7 0.5 - - - +
126V CYS 4.2 17.9 - - - +
127V THR* 4.9 1.3 - - - -
128V VAL* 3.5 31.7 - - + +
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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