Contacts of the strand formed by residues 439 - 449 (chain A) in PDB entry 1NNC
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 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A VAL* 3.1 20.8 - - - +
117A THR 3.8 2.9 - - - +
118A ARG* 3.9 20.3 - - + +
136A GLN* 5.2 0.2 - - - +
148A THR* 3.1 23.8 + - - +
149A ILE* 3.5 16.2 - - + +
427A ILE* 3.8 18.6 - - + -
428A ARG 3.5 4.9 - - - -
430A ARG* 2.6 39.6 + - - +
438A TRP* 1.3 75.1 + - - +
440A SER* 1.3 64.1 + - - +
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Residues in contact with SER 440 (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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106A VAL* 4.8 2.9 - - - -
115A LEU 4.3 2.6 + - - -
116A VAL* 3.6 15.0 - - - -
117A THR* 3.2 29.2 + - - -
118A ARG* 4.4 1.5 - - - +
140A ILE* 4.5 12.8 - - - +
427A ILE* 3.3 7.6 - - - +
428A ARG* 3.0 30.1 + - - +
438A TRP* 3.7 17.4 - - - -
439A THR* 1.3 76.3 - - - +
441A ASN* 1.3 75.3 + - - +
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Residues in contact with ASN 441 (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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105A ALA* 3.9 12.6 - - - +
106A VAL* 3.9 11.7 - - - +
117A THR* 2.8 40.3 + - - -
118A ARG* 3.2 6.1 + - + -
120A PRO* 3.4 26.9 - - - +
167A PRO* 5.8 0.2 - - - +
425A GLU* 3.6 25.0 - - + +
426A LEU 3.0 15.9 - - - +
427A ILE* 4.0 1.6 - - + -
440A SER* 1.3 85.6 + - - +
442A SER* 1.3 82.1 + - - +
443A ILE* 3.9 2.4 - - - +
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Residues in contact with SER 442 (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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102A LYS* 4.9 1.7 + - - -
103A ASP* 3.5 13.7 - - - -
104A ASN* 4.4 4.8 - - - -
105A ALA* 3.7 18.8 - - - -
106A VAL 4.3 1.3 - - - -
425A GLU* 3.8 0.9 - - - -
426A LEU* 3.0 40.5 + - - +
441A ASN* 1.3 86.2 + - - +
443A ILE* 1.3 66.3 + - - +
460A ASP* 2.6 30.2 + - - +
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Residues in contact with ILE 443 (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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102A LYS* 3.4 10.0 - - - +
103A ASP* 2.9 34.3 + - - +
120A PRO* 3.6 32.8 - - + -
121A TYR 4.8 2.9 - - - +
122A VAL* 4.9 1.1 - - + -
131A PHE* 3.7 47.1 - - + -
132A TYR 4.5 1.6 - - - +
161A TRP* 3.8 17.7 - - + -
423A TYR* 4.1 17.3 - - + -
424A VAL 3.6 7.4 - - - +
426A LEU* 4.4 3.8 - - - +
441A ASN* 3.9 2.7 - - - +
442A SER* 1.3 82.8 + - - +
444A VAL* 1.3 76.0 + - - +
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Residues in contact with VAL 444 (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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99A ILE* 3.7 20.9 - - + -
101A GLY 3.4 5.2 - - - +
102A LYS* 4.6 7.9 - - + -
397A ILE* 4.7 7.4 - - + -
398A VAL* 4.8 0.7 - - + -
423A TYR* 3.2 4.0 - - - +
424A VAL* 2.8 56.2 + - + +
426A LEU* 4.1 19.7 - - + -
443A ILE* 1.3 76.1 - - - +
445A SER* 1.3 64.4 + - - +
446A MET* 4.8 4.9 - - + -
458A TRP* 3.7 33.2 - - + +
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Residues in contact with SER 445 (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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99A ILE* 3.7 6.4 - - - +
100A TYR* 2.9 39.1 + - - -
101A GLY* 2.8 32.4 + - - +
122A VAL* 4.4 5.8 - - - -
131A PHE* 4.3 4.0 - - - -
410A PHE* 4.3 7.2 - - - -
422A PHE* 3.2 16.8 - - - -
423A TYR* 4.0 10.8 - - - +
443A ILE* 4.8 2.7 - - - -
444A VAL* 1.3 75.3 - - - +
446A MET* 1.3 63.3 + - - +
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Residues in contact with MET 446 (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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97A TRP* 3.5 40.2 - - + +
98A HIS 3.1 15.5 - - - +
99A ILE* 4.1 10.5 - - - +
100A TYR* 3.9 1.8 - - - -
395A GLN* 3.6 9.9 - - - +
397A ILE* 4.1 23.6 - - + -
410A PHE* 4.8 0.2 - - - -
421A CYS* 3.2 4.3 - - - +
422A PHE* 2.9 65.3 + - + +
444A VAL* 4.8 2.7 - - + -
445A SER* 1.3 81.0 - - - +
447A CYS* 1.3 65.2 + - - +
458A TRP* 4.3 21.1 - - + +
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Residues in contact with CYS 447 (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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97A TRP* 3.4 6.6 - - - -
98A HIS* 2.8 50.8 + - + +
100A TYR* 3.6 33.8 - - + +
419A ARG* 3.9 10.5 - - - -
420A ALA 3.2 5.6 - - - +
421A CYS* 2.0 46.4 - - - +
446A MET* 1.3 73.9 - - - +
448A SER* 1.3 61.6 + - - +
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Residues in contact with SER 448 (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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92A CYS* 4.8 7.4 - - - +
93A THR 4.8 0.7 + - - -
94A ILE* 3.6 41.1 - - - +
96A SER 3.4 5.4 - - - -
97A TRP* 3.5 6.0 - - - -
98A HIS* 3.7 0.9 + - - -
419A ARG* 3.3 34.3 + - - +
420A ALA 2.7 32.5 + - - -
447A CYS* 1.3 75.5 - - - +
449A SER* 1.3 60.8 + - - +
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Residues in contact with SER 449 (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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93A THR 3.6 3.0 - - - +
95A ASN 2.9 24.1 + - - -
96A SER* 2.9 20.2 + - - -
98A HIS* 4.2 9.2 - - - -
419A ARG* 5.0 3.8 - - - +
448A SER* 1.3 75.2 - - - +
450A THR* 1.3 63.4 + - - +
451A GLU* 3.0 26.5 + - - +
453A LEU* 3.8 24.7 - - - +
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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