Contacts of the strand formed by residues 121 - 128 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.4 23.4 - - - +
38A GLY 4.5 1.4 + - - +
51A VAL* 4.0 15.0 - - + +
54A GLU* 3.7 29.1 - - + +
55A ALA* 3.7 16.8 - - + +
58A ALA* 5.3 3.0 - - + +
81A VAL* 4.3 5.6 - - + -
82A LEU 3.3 13.2 - - - +
83A LEU* 4.0 14.1 - - + -
92A VAL* 4.4 9.9 - - + -
115A LEU* 3.4 4.9 - - - +
120A ARG* 1.3 83.0 + - - +
122A GLU* 1.3 66.0 + - - +
123A ILE* 4.2 19.5 - - + -
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Residues in contact with GLU 122 (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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35A GLY* 3.4 23.6 - - - +
36A GLN 3.3 22.7 - - - +
37A LEU* 3.6 15.2 - - + +
80A THR 3.6 0.9 - - - +
82A LEU* 2.8 49.9 + - + +
115A LEU* 3.4 28.5 - - + +
116A PRO* 3.5 18.9 - - - +
121A VAL* 1.3 77.0 - - - +
123A ILE* 1.3 66.2 + - - +
108C ALA* 4.4 14.9 - - - +
109C ALA 4.0 7.8 + - - +
110C TYR* 5.0 0.2 - - - -
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Residues in contact with ILE 123 (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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34A SER 4.0 0.9 - - - +
35A GLY* 4.1 0.9 - - - -
36A GLN* 2.8 35.2 + - - +
55A ALA* 4.9 3.1 - - - +
58A ALA* 4.6 10.3 - - + -
59A LEU* 4.0 33.2 - - + -
62A ILE* 3.7 27.6 - - + +
79A ALA* 4.7 9.0 - - + -
80A THR 3.3 14.4 - - - +
81A VAL* 4.3 19.1 - - + -
92A VAL* 5.1 5.8 - - + -
96A TYR* 4.7 7.6 - - + -
121A VAL* 4.2 17.5 - - + -
122A GLU* 1.3 79.7 - - - +
124A GLU* 1.3 68.5 + - - +
125A ALA* 5.2 0.9 - - + -
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Residues in contact with GLU 124 (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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33A ILE 3.9 9.4 - - - +
34A SER 4.4 0.7 - - - -
35A GLY* 3.8 18.8 - - - +
62A ILE* 5.2 0.2 - - - -
79A ALA* 3.4 1.0 - - - -
80A THR* 2.9 58.6 + - - +
82A LEU* 4.3 13.8 - - + +
122A GLU* 4.3 0.4 - - + -
123A ILE* 1.3 78.4 - - - +
125A ALA* 1.3 63.5 + - - +
78C LYS* 2.8 34.0 + - - +
80C THR* 4.6 3.2 + - - +
108C ALA* 4.0 16.8 - - - +
110C TYR* 4.4 6.9 + - - -
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Residues in contact with ALA 125 (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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33A ILE* 3.1 49.7 + - + +
62A ILE* 4.8 14.3 - - + +
76A VAL* 4.3 18.4 - - + -
78A LYS 3.3 12.6 - - - +
79A ALA* 4.5 4.9 - - + -
123A ILE* 5.2 0.9 - - + -
124A GLU* 1.3 78.7 - - - +
126A ILE* 1.3 68.2 + - - +
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Residues in contact with ILE 126 (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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30A THR* 3.9 21.8 - - + -
31A ILE 3.3 8.7 - - - +
32A TYR* 4.0 28.3 - - + -
76A VAL* 3.6 3.9 - - - -
77A VAL* 2.9 37.3 + - + +
78A LYS* 2.8 29.5 + - + +
125A ALA* 1.3 80.3 - - - +
127A ALA* 1.3 64.5 + - - +
128A VAL* 5.3 0.4 - - + -
32B TYR* 3.9 28.5 - - + +
126B ILE* 5.7 3.6 - - + -
78C LYS* 5.8 6.1 - - - +
126C ILE* 5.7 3.1 - - + -
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Residues in contact with ALA 127 (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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30A THR* 3.5 5.5 - - - +
31A ILE* 2.7 52.2 + - + +
33A ILE* 4.9 2.0 - - + +
66A LEU* 3.7 30.1 - - + -
75A ASN* 3.2 20.2 - - + +
76A VAL* 4.2 2.7 - - + -
77A VAL 4.4 0.2 - - - +
126A ILE* 1.3 75.5 - - - +
128A VAL* 1.3 64.6 + - - +
129A GLN 4.2 0.2 - - - -
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Residues in contact with VAL 128 (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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29A ARG* 3.3 11.2 - - + +
30A THR* 4.4 15.3 - - + +
71A CYS* 4.8 0.9 - - - -
75A ASN* 3.0 31.0 + - - +
77A VAL* 4.1 13.5 - - + -
126A ILE* 5.3 0.2 - - + -
127A ALA* 1.3 79.2 - - - +
129A GLN* 1.3 69.9 + - - +
130A GLY 3.3 0.2 + - - -
132A LEU* 4.0 11.4 - - + +
4B LEU* 3.8 24.2 - - + -
27B VAL* 3.7 44.0 - - + -
28B ASP* 6.0 0.2 - - + -
32B TYR* 5.5 1.3 - - + -
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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