Contacts of the strand formed by residues 30 - 36 (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 THR 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL 3.6 2.1 - - - +
26A LEU* 3.5 1.0 - - - -
27A VAL* 3.0 35.5 + - - +
28A ASP* 5.7 0.7 - - - +
29A ARG* 1.3 80.4 + - - +
31A ILE* 1.3 65.0 + - - +
32A TYR* 3.7 34.4 + - + +
126A ILE* 3.9 16.8 - - + -
127A ALA 3.5 8.5 - - - +
128A VAL* 4.4 10.7 - - + +
32B TYR* 4.5 7.0 + - - +
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Residues in contact with ILE 31 (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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9A ILE* 5.1 0.9 - - + -
24A ALA* 4.2 11.4 - - + -
25A VAL 3.4 9.9 - - - +
26A LEU* 3.8 21.1 - - + -
29A ARG 4.3 3.6 - - - +
30A THR* 1.3 76.7 - - - +
32A TYR* 1.3 64.4 + - - +
33A ILE* 3.7 22.1 + - + +
65A ILE* 5.7 1.1 - - + -
66A LEU* 5.1 2.9 - - + -
69A ALA* 3.9 22.9 - - + +
71A CYS* 3.5 33.0 - - + -
125A ALA 3.9 0.3 - - - +
126A ILE* 3.3 8.5 - - - +
127A ALA* 2.7 48.0 + - + +
129A GLN* 4.4 7.2 - - + +
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Residues in contact with TYR 32 (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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24A ALA* 3.2 3.3 - - - -
25A VAL 2.9 39.3 + - - +
27A VAL* 4.0 14.8 - - + -
30A THR* 3.7 26.0 - - + +
31A ILE* 1.3 72.8 - - - +
33A ILE* 1.3 59.8 + - - +
125A ALA 4.3 1.8 - - - -
126A ILE* 4.0 28.7 - - + -
32B TYR* 4.6 5.6 + - - -
30C THR* 4.4 10.7 + - - +
32C TYR* 4.6 5.9 + + - -
77C VAL* 3.9 27.6 - - + +
78C LYS* 4.0 31.6 - - + -
106C ALA* 3.3 11.7 - - + +
126C ILE* 3.8 33.4 - - + +
128C VAL* 5.5 1.7 - - + +
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Residues in contact with ILE 33 (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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23A GLN 3.7 11.7 - - - +
24A ALA* 3.9 4.7 - - + -
31A ILE* 4.0 17.0 - - + +
32A TYR* 1.3 74.3 - - - +
34A SER* 1.3 76.8 + - - +
35A GLY 3.7 0.7 + - - -
36A GLN* 4.6 7.9 - - + -
62A ILE* 4.2 17.5 - - + -
65A ILE* 4.0 22.2 - - + -
66A LEU* 3.7 35.7 - - + -
124A GLU* 3.9 5.1 - - - +
125A ALA* 3.1 42.4 + - + +
127A ALA* 4.9 3.1 - - + -
78C LYS* 5.1 6.7 + - - +
106C ALA* 4.3 1.8 - - - -
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Residues in contact with SER 34 (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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21A TYR* 3.8 13.5 - - - -
22A SER 2.6 24.5 + - - -
23A GLN* 3.0 18.0 + - - -
33A ILE* 1.3 83.4 - - - +
35A GLY* 1.3 68.8 + - - +
36A GLN* 3.3 15.1 + - - +
123A ILE 4.0 2.4 - - - +
124A GLU* 4.4 0.2 - - - -
78C LYS* 5.7 1.1 - - - +
106C ALA* 3.2 4.0 - - - +
107C ARG 2.7 36.9 + - - +
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Residues in contact with GLY 35 (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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21A TYR* 5.9 1.4 - - - -
33A ILE 3.7 0.8 + - - -
34A SER* 1.3 75.2 - - - +
36A GLN* 1.3 65.9 + - - +
37A LEU* 4.2 1.9 + - - +
122A GLU* 3.4 24.5 - - - +
123A ILE 3.5 9.0 - - - -
124A GLU* 3.8 14.9 - - - +
107C ARG 3.0 14.1 + - - +
108C ALA* 4.3 3.1 - - - +
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Residues in contact with GLN 36 (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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14A ALA* 4.7 4.8 - - - +
15A PRO* 3.5 24.7 + - - +
21A TYR* 5.9 1.2 - - - -
23A GLN* 4.8 7.5 - - - +
33A ILE* 4.6 3.8 - - + -
34A SER* 3.4 21.2 - - - +
35A GLY* 1.3 86.3 - - - +
37A LEU* 1.3 62.6 - - - +
58A ALA* 3.8 21.8 - - - +
61A ASN* 3.4 25.2 + - + +
62A ILE* 3.7 24.0 - - + +
65A ILE* 4.9 8.6 - - + +
122A GLU* 3.3 7.9 - - - +
123A ILE 2.8 36.2 + - - +
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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