Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 1D6W
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 LYS 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL 3.7 0.7 - - - +
67A ARG* 3.6 0.7 - - - -
68A ILE* 2.7 41.7 + - - +
78A ASN 4.5 8.0 + - - -
79A ILE* 2.6 26.9 + - - +
80A GLU* 1.3 76.7 - - - +
82A ILE* 1.3 62.3 + - - +
83A SER* 5.0 1.6 - - - +
112A VAL* 4.1 16.6 - - + -
113A ALA* 4.7 7.4 - - + +
115A SER* 3.0 33.3 + - - -
117A TYR* 4.6 4.0 - - - -
118A ILE* 2.7 30.2 - - + +
363I TYS 3.7 10.3 - - - +
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Residues in contact with ILE 82 (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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65A LEU* 3.7 29.4 - - + -
66A VAL 3.2 6.7 - - - +
67A ARG* 3.9 16.8 - - + +
76A TYR* 3.8 22.0 - - + -
80A GLU* 3.6 22.0 - - - +
81A LYS* 1.3 75.0 - - - +
83A SER* 1.3 65.0 + - - +
359I ILE* 3.9 25.1 - - + -
363I TYS 3.4 55.4 + - + +
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Residues in contact with SER 83 (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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65A LEU* 3.5 10.6 - - - +
66A VAL* 2.6 41.7 + - - +
68A ILE* 4.3 7.4 - - - +
81A LYS* 4.8 1.7 + - - +
82A ILE* 1.3 78.2 + - - +
84A MET* 1.3 65.7 - - - +
108A LEU* 3.9 36.7 - - - +
109A LYS 5.6 0.2 - - - -
110A LYS 4.5 7.1 + - - -
112A VAL* 4.8 7.6 - - - +
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Residues in contact with MET 84 (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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36A LYS* 4.9 9.9 - - - +
64A LEU 5.0 0.4 - - - +
65A LEU* 4.0 19.7 - - + -
83A SER* 1.3 77.7 - - - +
85A LEU* 1.3 60.8 + - - +
108A LEU* 3.4 7.3 - - - +
109A LYS* 2.7 71.5 + - + +
362I GLU 5.7 2.9 - - - +
363I TYS 4.5 17.0 - - + +
364I LEU 5.7 3.4 - - - +
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Residues in contact with LEU 85 (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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61A GLU* 3.6 43.9 + - + +
62A ASN* 5.5 1.0 - - - +
64A LEU* 4.0 26.7 - - + +
66A VAL* 3.6 29.4 - - + +
83A SER 4.7 0.4 - - - +
84A MET* 1.3 82.5 - - - +
86A GLU* 1.3 61.1 + - - +
87A LYS 4.5 4.3 - - - +
88A ILE* 4.5 3.4 - - + -
106A MET* 3.0 41.3 - - + -
107A LYS 3.7 4.3 - - - +
108A LEU* 3.8 14.1 - - + -
109A LYS* 4.2 12.7 - - - +
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Residues in contact with GLU 86 (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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50A ARG* 3.2 24.4 + - - -
61A GLU* 3.4 13.7 - - - +
85A LEU* 1.3 75.1 - - - +
87A LYS* 1.3 64.5 + - + +
107A LYS* 2.6 48.0 + - + +
108A LEU 4.0 8.5 - - - +
109A LYS* 3.9 16.7 - - + +
110A LYS* 5.5 1.4 + - - -
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Residues in contact with LYS 87 (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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61A GLU* 3.1 19.2 + - - +
85A LEU* 3.7 2.0 - - - +
86A GLU* 1.3 87.9 - - + +
88A ILE* 1.3 88.3 + - - +
89A TYR* 3.1 41.0 - - + +
105A LEU 3.8 0.5 - - - +
106A MET* 3.2 4.7 - - - +
107A LYS* 2.8 38.6 + - + +
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Residues in contact with ILE 88 (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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59A LEU* 3.0 46.4 - - + -
60A PHE 3.8 39.3 - - + -
61A GLU* 3.1 20.7 + - + +
64A LEU* 4.7 0.4 - - + -
85A LEU* 4.5 2.5 - - + -
87A LYS* 1.3 101.4 + - - +
89A TYR* 1.3 66.4 + - - +
90A ILE* 4.1 15.4 + - + +
105A LEU 3.4 4.7 - - - +
106A MET* 4.2 15.9 - - + -
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Residues in contact with TYR 89 (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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51A TRP* 3.9 32.3 - + - -
87A LYS* 3.1 49.1 - - + +
88A ILE* 1.3 76.8 - - - +
90A ILE* 1.3 62.1 + - - +
104A ALA* 3.0 6.0 - - - -
105A LEU* 2.7 49.4 + - + +
107A LYS* 4.5 3.6 - - + +
237A TRP* 3.3 13.9 - - + -
241A VAL* 4.1 8.7 - - + -
245A PHE* 3.5 55.8 - + - +
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Residues in contact with ILE 90 (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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56A ALA* 3.7 25.8 - - + +
59A LEU* 3.8 40.2 - - + -
60A LEU* 4.4 17.9 - - + -
88A ILE* 4.1 9.2 + - + +
89A TYR* 1.3 75.8 - - - +
91A HIS* 1.3 77.5 + - - +
92A PRO* 3.1 8.1 - - - +
94A TYR* 3.8 15.0 - - + -
103A ILE 3.9 2.0 - - - -
104A ALA* 3.9 7.6 - - + -
237A TRP* 3.6 5.1 + - - -
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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