Contacts of the strand formed by residues 121 - 128 (chain C) in PDB entry 1NQ3
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 VAL 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLN 4.0 0.5 - - - +
37C LEU* 3.7 20.4 - - - +
38C GLY 4.3 1.6 + - - -
51C VAL* 4.0 13.0 - - + +
54C GLU* 3.7 16.4 + - + +
55C ALA* 3.7 31.6 - - + +
58C ALA* 5.1 2.4 - - + +
81C VAL* 4.2 6.3 - - + -
82C LEU 3.3 12.6 - - - +
83C LEU* 4.2 13.9 - - + -
92C VAL* 4.3 11.0 - - + -
115C LEU* 3.6 3.7 - - - +
119C GLY 3.5 1.0 - - - -
120C ARG* 1.3 82.9 - - - +
122C GLU* 1.3 65.2 + - - +
123C ILE* 4.2 20.0 - - + -
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA* 4.1 18.4 - - - +
109B ALA 3.8 7.6 + - - +
110B TYR* 4.5 0.2 - - - -
35C GLY* 3.5 20.6 - - - +
36C GLN 3.3 20.2 - - - +
37C LEU* 3.5 23.9 - - + +
80C THR 3.7 1.0 - - - +
82C LEU* 2.8 49.5 + - + +
115C LEU* 3.7 17.2 - - + +
116C PRO* 3.5 20.1 - - - +
121C VAL* 1.3 75.5 - - - +
123C ILE* 1.3 68.2 + - - +
124C GLU* 5.5 0.2 - - - +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C SER 4.0 1.0 - - - +
35C GLY* 3.4 1.3 - - - -
36C GLN 2.8 32.4 + - - +
55C ALA* 4.8 3.1 - - - +
58C ALA* 4.4 12.6 - - + -
59C LEU* 3.6 35.0 - - + -
62C ILE* 3.7 27.7 - - + +
79C ALA* 4.8 7.6 - - + -
80C THR 3.3 13.0 - - - +
81C VAL* 4.5 19.3 - - + -
92C VAL* 5.2 6.1 - - + -
96C TYR* 4.9 6.5 - - + -
121C VAL* 4.2 15.9 - - + -
122C GLU* 1.3 80.8 - - - +
124C GLU* 1.3 67.5 + - - +
125C ALA* 5.3 0.7 - - + -
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Residues in contact with GLU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 2.9 32.3 + - - -
80B THR* 4.7 2.7 + - - +
108B ALA* 3.7 17.5 - - - +
110B TYR* 4.4 8.1 + - - -
33C ILE 3.9 8.1 - - - +
34C SER 4.5 0.7 - - - -
35C GLY* 3.7 18.6 - - - +
79C ALA* 3.4 1.4 - - - -
80C THR* 2.9 61.3 + - + +
82C LEU* 4.4 12.4 - - + +
122C GLU* 4.3 0.8 - - - +
123C ILE* 1.3 76.9 - - - +
125C ALA* 1.3 65.1 + - - +
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 5.9 0.9 - - - -
33C ILE* 3.0 51.5 + - + +
62C ILE* 4.8 15.3 - - + -
76C VAL* 4.2 16.8 - - + -
78C LYS* 3.3 11.9 - - - +
79C ALA* 4.3 5.2 - - + +
123C ILE* 4.4 0.9 + - + -
124C GLU* 1.3 78.7 - - - +
126C ILE* 1.3 68.9 - - - +
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.8 31.6 - - + +
126A ILE* 5.7 2.9 - - + -
78B LYS* 6.3 2.0 - - - -
30C THR* 3.9 22.0 - - + -
31C ILE 3.3 8.5 - - - +
32C TYR* 4.2 24.7 - - + -
76C VAL* 3.5 3.9 - - - +
77C VAL* 2.9 34.0 + - + +
78C LYS* 2.9 31.5 + - + +
125C ALA* 1.3 81.4 - - - +
127C ALA* 1.3 63.9 + - - +
128C VAL* 5.3 0.7 - - + -
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C THR* 3.5 2.6 - - - +
31C ILE* 2.6 50.9 + - + +
33C ILE* 4.6 2.0 - - + -
66C LEU* 3.8 27.6 - - + -
75C ASN* 3.1 24.5 - - + +
76C VAL* 4.0 3.4 - - + -
77C VAL 4.2 0.9 - - - +
125C ALA 4.3 0.2 - - - -
126C ILE* 1.3 74.1 - - - +
128C VAL* 1.3 67.4 + - - +
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.7 29.6 - - + -
27A VAL* 4.0 32.1 - - + -
32A TYR* 5.5 1.8 - - + +
29C ARG 3.3 11.0 - - - +
30C THR* 4.4 15.7 - - + +
71C CYS* 4.8 1.3 - - - -
75C ASN* 2.9 32.5 + - - +
77C VAL* 4.1 14.8 - - + -
126C ILE* 5.3 0.2 - - + -
127C ALA* 1.3 79.6 - - - +
129C GLN* 1.3 67.5 + - - +
132C LEU* 3.5 17.5 - - + +
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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