Contacts of the strand formed by residues 96 - 102 (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 SER 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ILE* 3.5 5.6 - - - +
95A ASN* 1.3 81.4 - - - +
97A TRP* 1.3 71.6 + - - +
361A TRP* 4.7 3.4 - - - -
392A GLN* 5.0 1.3 - - - -
395A GLN* 3.6 15.9 - - - +
448A SER* 3.4 5.5 - - - -
449A SER* 2.9 25.0 + - - +
451A GLU 2.6 22.3 + - - -
452A PHE* 4.1 0.9 - - - -
453A LEU* 2.9 35.2 + - - +
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Residues in contact with TRP 97 (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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94A ILE* 3.5 25.3 - - + +
96A SER* 1.3 83.8 - - - +
98A HIS* 1.3 59.3 + - - +
354A TYR* 4.2 10.1 - + - -
361A TRP* 3.3 42.1 - + + -
376A MET* 3.7 31.6 - - + +
395A GLN* 3.0 33.9 + - - +
397A ILE* 5.0 0.4 - - + -
420A ALA* 3.4 41.5 - - + -
421A CYS* 4.3 0.7 - - - -
422A PHE* 3.4 32.5 - + + -
446A MET* 3.5 22.0 - - + +
447A CYS* 3.4 23.6 - - - +
448A SER* 3.5 3.8 - - - -
449A SER* 5.1 0.2 - - - -
453A LEU* 4.5 9.0 - - - +
454A GLY 5.1 2.6 - - - +
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Residues in contact with HIS 98 (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* 1.3 73.9 - - - +
99A ILE* 1.3 90.2 + - + +
100A TYR* 4.3 8.3 - - - -
419A ARG* 2.9 34.2 + - - -
446A MET* 3.1 8.9 - - - -
447A CYS* 2.8 60.5 + - + +
448A SER 3.7 7.5 + - - -
449A SER* 4.2 4.9 - - - -
453A LEU* 3.6 23.8 - - + +
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Residues in contact with ILE 99 (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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98A HIS* 1.3 87.0 - - + +
100A TYR* 1.3 60.5 + - - +
101A GLY* 4.1 11.4 - - - +
102A LYS* 4.7 4.5 - - + -
444A VAL* 3.7 23.8 - - + -
445A SER 3.7 16.6 - - - +
446A MET* 4.1 7.3 - - - +
458A TRP* 3.7 50.9 - - + +
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Residues in contact with TYR 100 (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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98A HIS* 3.4 8.0 + - - +
99A ILE* 1.3 76.3 - - - +
101A GLY* 1.3 57.0 + - - +
122A VAL* 4.6 1.8 - - + -
129A CYS* 3.3 33.8 - - - +
163A LEU* 3.5 40.7 - - + +
164A SER* 4.4 1.4 + - - -
410A PHE* 3.8 25.1 - + - -
412A ASP* 5.6 1.9 - - + +
421A CYS* 5.6 0.2 - - - -
445A SER* 2.9 39.0 + - - +
446A MET* 3.9 7.6 - - - -
447A CYS* 3.6 24.7 - - + +
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Residues in contact with GLY 101 (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* 4.1 3.1 - - - +
100A TYR* 1.3 85.6 - - - +
102A LYS* 1.3 62.4 + - - +
131A PHE* 4.1 10.3 - - - -
163A LEU* 4.9 2.0 - - - -
164A SER* 3.1 13.7 - - - -
444A VAL* 3.4 2.6 - - - +
445A SER* 2.8 40.9 + - - +
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Residues in contact with LYS 102 (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* 4.7 9.0 - - + -
101A GLY* 1.3 75.5 - - - +
103A ASP* 1.3 62.6 + - - +
104A ASN* 2.9 40.3 + - - +
131A PHE* 4.2 1.0 - - - -
164A SER* 3.1 22.6 + - - +
426A LEU* 4.8 3.6 - - - +
442A SER* 4.9 1.8 + - - -
443A ILE 3.4 14.1 - - - +
444A VAL* 4.6 6.1 - - + -
458A TRP* 3.8 40.2 - - + +
459A PRO* 2.9 30.3 + - - -
460A ASP* 3.5 10.9 + - - +
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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