Contacts of the strand formed by residues 124 - 128 (chain E) in PDB entry 1NVI
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 PHE 124 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D VAL* 3.5 2.8 - - - -
79D THR 2.9 23.4 + - - -
80D GLY* 3.5 21.1 - - - -
8E VAL* 4.2 15.3 - - + -
52E LEU* 4.0 6.7 - - + -
53E GLU 3.3 6.3 - - - -
54E HIS* 3.7 20.0 - - + -
59E THR* 4.4 10.3 - - + -
63E LEU* 4.6 9.4 - - + -
83E HIS* 3.5 55.2 - + + -
85E ILE* 3.8 22.9 - - + -
118E LEU* 5.0 1.1 - - + -
122E ALA* 2.9 32.6 + - + +
123E PRO* 1.3 74.2 - - - +
125E TRP* 1.3 68.9 + - - +
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Residues in contact with TRP 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.5 34.8 - + + -
8D ALA* 3.7 14.6 - - + -
9D GLN* 5.3 0.7 - - - -
75D PHE* 3.4 32.3 - + + -
76D PRO* 3.1 28.1 + - + +
77D PRO 3.5 19.0 + - - -
78D VAL* 3.9 3.8 - - + +
79D THR* 3.3 7.9 - - + +
51E THR 3.5 2.9 - - - +
52E LEU* 3.5 2.9 - - - +
53E GLU* 2.9 53.9 + - + +
54E HIS 3.7 13.9 - - - -
55E TYR* 4.2 2.5 - - + -
123E PRO* 3.7 36.1 - - + -
124E PHE* 1.3 81.4 + - - +
126E LYS* 1.3 62.2 + - - +
127E ARG 4.0 0.2 + - - -
136E TRP* 3.7 21.7 - - + -
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Residues in contact with LYS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D THR* 2.9 33.0 + - - +
80D GLY* 4.2 2.6 + - - -
81D GLY* 2.6 31.0 + - - -
50E LEU* 4.0 24.4 - - + +
51E THR 3.5 4.7 - - - -
52E LEU* 3.7 16.4 - - + -
94E ILE* 3.5 20.6 - - - +
119E LYS* 4.6 3.6 - - - +
125E TRP* 1.3 72.1 - - - +
127E ARG* 1.3 59.3 + - - +
128E GLU 4.3 0.2 - - - -
136E TRP* 3.3 8.6 - - - -
137E VAL* 3.0 45.5 + - + +
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Residues in contact with ARG 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ARG* 5.4 3.8 - - - +
12D GLU* 4.1 11.6 + - - -
49E ALA 4.1 0.3 - - - +
50E LEU* 3.3 4.0 - - - +
51E THR* 2.8 74.7 + - - +
125E TRP 4.0 0.2 + - - -
126E LYS* 1.3 75.0 - - - +
128E GLU* 1.3 64.6 + - - +
134E ASP* 3.3 47.9 + - + -
135E ARG 3.7 9.0 - - - +
136E TRP* 3.7 43.9 - - + +
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ASN* 6.0 1.6 - - + +
49E ALA 3.6 6.5 - - - -
50E LEU* 3.4 24.3 - - + +
127E ARG* 1.3 72.9 - - - +
129E ALA* 1.3 60.7 + - - +
130E THR* 4.8 11.8 - - + +
134E ASP* 3.3 12.4 - - - +
135E ARG* 2.8 59.5 + - + +
137E VAL* 3.5 24.8 - - + +
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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