Contacts of the strand formed by residues 102 - 107 (chain A) in PDB entry 4NKT
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 MET 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.4 61.7 - - + +
66A ARG* 6.5 0.7 - - - -
68A ALA* 4.1 4.7 - - - -
69A LEU* 4.1 13.5 - - + +
72A LEU* 5.5 0.2 - - - -
87A ALA* 5.6 2.2 - - + -
91A LEU* 4.0 12.3 - - + -
101A ASP* 1.3 79.1 - - - +
103A ASP* 1.3 64.7 + - - +
104A LEU* 4.0 24.2 - - + -
157A PHE* 3.9 22.9 - - + -
158A GLN 3.1 11.0 + - - +
159A CYS* 3.6 15.2 - - - -
160A ALA* 3.0 24.8 + - - +
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Residues in contact with ASP 103 (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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87A ALA* 3.7 0.9 - - - +
88A PHE* 3.1 61.3 + - + +
89A GLY* 4.5 3.6 - - - -
90A SER* 5.0 1.2 + - - -
91A LEU* 5.1 1.8 - - - +
101A ASP* 4.1 4.5 + - - +
102A MET* 1.3 77.8 - - - +
104A LEU* 1.3 66.3 + - - +
160A ALA* 3.6 16.2 - - - +
401A 2KH 3.6 36.5 + - - +
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Residues in contact with LEU 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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69A LEU* 3.9 16.4 - - + -
72A LEU* 3.6 21.5 - - + -
85A LEU* 3.9 26.2 - - + -
86A VAL 3.4 4.7 - - - +
87A ALA* 3.7 24.7 - - + -
88A PHE* 3.5 8.8 - - - -
102A MET* 4.0 17.3 - - + -
103A ASP* 1.3 84.5 - - - +
105A CYS* 1.3 62.1 + - - +
159A CYS* 3.5 27.6 - - - -
160A ALA 2.8 12.1 + - - +
161A ILE* 4.2 8.5 - - + -
162A GLY 2.9 23.6 + - - -
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Residues in contact with CYS 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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84A GLU 3.6 0.7 - - - +
85A LEU* 3.6 4.7 - - - -
86A VAL* 2.8 42.4 + - - +
88A PHE* 3.9 15.5 - - + -
104A LEU* 1.3 78.8 - - - +
106A VAL* 1.3 62.1 + - - +
107A LEU* 3.6 21.6 + - - -
162A GLY 3.4 5.8 - - - -
164A ASN 4.0 2.9 - - - -
165A ASN* 3.4 37.5 - - - -
169A ILE* 3.8 15.5 - - + -
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Residues in contact with VAL 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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76A LEU* 4.2 6.5 - - + -
83A ALA* 4.3 9.9 - - + -
84A GLU 3.3 7.9 - - - +
85A LEU* 3.8 19.5 - - + +
105A CYS* 1.3 70.6 - - - +
107A LEU* 1.3 58.2 + - - +
108A MET* 4.2 20.1 - - + +
117A ILE* 4.2 8.1 - - + -
121A PHE* 3.8 20.9 - - + -
161A ILE* 3.9 5.6 - - + -
162A GLY 2.8 9.5 + - - -
163A PHE* 3.5 36.3 - - + +
164A ASN* 2.8 33.1 + - - +
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Residues in contact with LEU 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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82A ASP 3.8 1.7 - - - +
83A ALA* 3.5 1.9 - - - -
84A GLU* 2.8 38.4 + - + +
86A VAL* 3.7 20.9 - - + -
105A CYS* 3.6 23.8 - - - -
106A VAL* 1.3 71.4 - - - +
108A MET* 1.3 66.2 + - - +
164A ASN* 3.4 18.6 - - - +
166A ARG* 3.9 32.5 - - + +
169A ILE* 3.6 22.7 - - + -
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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