Contacts of the strand formed by residues 101 - 108 (chain A) in PDB entry 5NKS
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 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLY 3.5 8.1 - - - +
71A ASP* 3.9 12.1 - - + -
96A ALA* 2.9 27.5 + - + +
97A LEU* 3.1 28.4 + - - +
99A GLY 4.6 0.5 + - - -
100A GLY* 1.3 79.2 - - - +
102A THR* 1.3 59.7 + - - +
103A MET 3.3 26.5 - - - +
104A ILE* 4.2 0.7 - - + -
133A CYS* 4.7 0.5 - - - -
358A ILE* 4.4 8.1 + - + -
361A ARG* 2.9 30.2 + - - +
362A MET* 3.8 7.3 - - - +
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 3.2 32.3 + - - -
69A GLY 2.9 3.8 + - - +
70A VAL* 5.7 0.3 - - - +
97A LEU* 3.9 12.6 - - + -
100A GLY 4.7 0.7 - - - +
101A THR* 1.3 77.7 - - - +
103A MET* 1.3 62.9 + - - +
133A CYS* 3.4 19.9 - - - +
134A ASP* 3.6 7.8 + - - +
408A ASP* 3.4 26.9 + - + +
409A LEU 4.7 0.9 - - - +
446A VAL* 3.9 19.7 - - + -
447A ILE 3.6 23.8 - - - +
448A SER* 4.4 4.5 + - - -
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Residues in contact with MET 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.1 2.8 + - - -
70A VAL* 3.4 16.7 - - + -
71A ASP 2.7 32.0 + - - -
101A THR* 3.3 6.7 - - - +
102A THR* 1.3 80.5 - - - +
104A ILE* 1.3 61.5 + - - +
105A LEU* 3.8 17.3 - - + -
133A CYS* 4.4 0.4 - - - -
134A ASP* 3.3 23.1 - - + +
135A TYR 3.9 2.9 - - - +
136A SER* 3.9 8.7 - - - -
394A PHE* 3.7 41.7 - - + -
398A LYS* 3.9 23.1 - - + -
469A VAL* 3.7 30.7 - - + -
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Residues in contact with ILE 104 (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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71A ASP* 3.4 6.1 - - + -
74A THR* 3.5 35.4 - - + +
76A LEU* 3.5 26.2 - - + -
89A PHE* 4.0 13.7 - - + -
93A THR* 3.6 19.1 - - + -
96A ALA* 4.2 16.2 - - + -
101A THR* 4.2 14.1 - - + -
103A MET* 1.3 81.6 - - - +
105A LEU* 1.3 65.2 + - - +
106A ASP 4.8 0.7 - - - +
133A CYS* 4.4 6.1 - - - -
134A ASP 3.3 3.7 + - - +
135A TYR* 3.2 18.9 - - + +
136A SER 3.0 23.6 + - - -
358A ILE* 4.2 2.5 - - + -
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Residues in contact with LEU 105 (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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70A VAL* 4.7 3.8 - - + -
71A ASP 2.8 13.8 + - - +
72A VAL* 3.6 18.8 - - + +
73A HIS* 3.6 5.4 - - - -
74A THR* 3.0 22.9 + - - -
103A MET* 3.8 14.8 - - + -
104A ILE* 1.3 75.1 - - - +
106A ASP* 1.3 62.1 + - - +
136A SER* 3.3 33.4 - - - -
138A HIS* 3.3 36.4 - - + +
392A PHE* 3.8 29.4 - - + -
394A PHE* 4.2 12.6 - - + -
471A ARG* 4.8 3.8 - - - +
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Residues in contact with ASP 106 (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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74A THR* 2.7 24.2 + - - +
75A ARG* 4.3 0.2 - - - -
76A LEU* 2.8 33.6 + - - +
77A GLN 4.3 1.4 + - - -
89A PHE* 3.6 32.2 - - + -
104A ILE* 3.9 1.3 - - + -
105A LEU* 1.3 74.4 - - - +
107A HIS* 1.3 63.4 + - - +
108A VAL 3.6 0.6 + - - -
123A TRP* 2.9 30.7 + - - -
136A SER 2.9 6.6 + - - +
137A LEU* 3.2 14.5 - - + +
138A HIS 2.8 31.5 + - - +
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Residues in contact with HIS 107 (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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72A VAL 4.6 0.2 + - - -
73A HIS* 3.3 43.4 + + - +
74A THR 3.0 14.2 + - - +
75A ARG* 3.4 34.5 + - + +
78A MET* 4.8 5.4 + - - +
105A LEU 4.4 1.1 - - - -
106A ASP* 1.3 73.3 - - - +
108A VAL* 1.3 63.0 + - - +
109A PHE* 3.5 3.5 + - - +
123A TRP* 3.3 21.2 + - - -
138A HIS* 3.4 26.3 + + - +
140A ASP* 2.6 24.6 + - - +
165A LEU* 3.8 9.6 - - + -
196A GLN* 3.2 30.9 + - - -
253A THR* 4.8 0.2 - - + -
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Residues in contact with VAL 108 (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 ASP 3.6 0.2 + - - -
107A HIS* 1.3 70.0 - - - +
109A PHE* 1.3 62.6 + - - +
110A PRO* 3.9 3.0 - - + +
116A LEU* 4.7 2.0 - - - +
119A ALA* 3.6 38.8 - - + +
120A TYR* 3.7 8.3 - - + +
123A TRP* 3.6 33.7 - - + -
137A LEU* 3.9 20.4 - - + -
138A HIS 2.8 20.3 + - - +
139A VAL* 4.1 18.6 - - + -
140A ASP* 2.8 33.8 + - - +
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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