Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 4ISN
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 GLN 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 ALA 3.6 0.7 - - - +
67A PHE* 3.5 2.9 - - - -
68A LEU* 2.8 49.7 + - + +
79A GLY* 3.8 8.4 + - - +
80A VAL* 1.3 79.0 - - - +
82A GLU* 1.3 60.7 + - - +
83A ARG* 3.3 24.1 + - + +
112A ALA* 3.8 7.3 - - - +
113A GLU* 2.6 60.3 + - - +
115A SER* 4.3 6.3 + - - -
118A VAL* 3.5 18.2 - - - +
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Residues in contact with GLU 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 THR* 3.5 28.8 + - + +
66A ALA 3.5 3.6 - - - -
67A PHE* 3.9 26.4 - - + -
76A ARG 5.3 2.1 - - - +
80A VAL* 4.2 2.2 + - + +
81A GLN* 1.3 73.7 - - - +
83A ARG* 1.3 80.6 + - - +
84A ARG* 6.4 0.7 - - + -
110A LYS* 5.3 1.0 + - - +
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Residues in contact with ARG 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 THR* 3.7 4.3 - - - -
66A ALA* 2.8 44.4 + - - +
68A LEU* 3.9 19.5 - - + -
81A GLN* 3.3 35.5 + - + +
82A GLU* 1.3 102.3 + - - +
84A ARG* 1.3 66.4 + - - +
108A LEU* 3.9 25.1 - - + -
110A LYS* 3.1 54.0 + - - +
111A PRO 3.0 29.5 + - - -
112A ALA* 4.1 1.2 - - - +
113A GLU* 3.9 10.7 + - - +
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Residues in contact with ARG 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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62A THR* 2.9 49.6 + - - +
64A TRP 4.2 13.2 + - - +
65A THR* 5.3 6.5 - - + +
82A GLU* 6.4 0.9 - - + -
83A ARG* 1.3 78.3 - - - +
85A LEU* 1.3 70.3 + - - +
108A LEU* 3.7 4.5 - - - -
109A GLU* 2.9 65.3 + - - +
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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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33A LEU* 3.9 13.9 - - + -
52A LEU* 4.5 2.2 - - + -
59A TYR* 5.3 0.2 - - + -
61A PRO* 3.5 32.9 + - + +
62A THR* 4.6 1.7 + - - +
64A TRP* 3.7 32.7 + - + +
66A ALA* 4.5 11.2 - - + -
83A ARG 5.1 1.1 - - - +
84A ARG* 1.3 88.8 + - - +
86A LYS* 1.3 61.1 + - - +
87A ARG 4.6 2.5 - - - +
88A ILE* 4.2 18.2 - - + -
106A LEU* 4.1 25.1 - - + -
107A GLU 3.4 12.3 - - - +
108A LEU* 4.1 19.1 - - + -
109A GLU* 4.2 8.4 - - - +
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Residues in contact with LYS 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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61A PRO* 3.9 12.3 - - - +
85A LEU* 1.3 73.2 - - - +
87A ARG* 1.3 60.4 + - + +
107A GLU* 2.7 43.0 + - + +
108A LEU 3.8 18.4 + - - +
109A GLU* 3.8 25.4 + - + +
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Residues in contact with ARG 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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51A TRP* 3.8 14.1 - - - -
61A PRO* 3.8 9.1 - - - +
85A LEU* 3.7 2.0 - - - +
86A LYS* 1.3 82.8 + - + +
88A ILE* 1.3 79.0 + - - +
89A ILE* 3.8 29.1 - - + +
105A LEU 3.9 0.2 - - - +
106A LEU* 3.6 3.5 - - - +
107A GLU* 2.9 56.2 + - + +
241A ASN* 4.6 5.9 + - - -
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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 TYR* 3.8 29.8 - - + +
60A SER* 3.7 44.7 - - + +
61A PRO* 3.8 22.9 - - + +
64A TRP* 4.0 12.3 - - + +
85A LEU* 4.2 8.7 - - + -
87A ARG* 1.3 82.7 - - - +
89A ILE* 1.3 65.1 + - - +
90A SER* 3.8 13.2 + - - +
104A ALA* 4.9 1.3 - - + -
105A LEU 3.5 3.1 - - - +
106A LEU* 3.8 21.3 - - + -
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Residues in contact with ILE 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 26.5 - - + -
87A ARG* 3.8 34.5 - - + +
88A ILE* 1.3 73.1 - - - +
90A SER* 1.3 65.1 + - - +
91A HIS 3.8 0.3 + - - -
92A PRO* 5.5 1.8 - - + -
104A ALA* 3.3 5.9 - - - -
105A LEU* 2.8 40.4 + - + +
237A TRP* 3.9 23.8 - - + +
241A ASN* 4.0 33.2 - - + +
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Residues in contact with SER 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* 3.9 26.2 + - - +
59A TYR* 4.6 6.6 + - - +
60A ILE* 4.6 11.6 - - - +
88A ILE* 3.8 10.7 + - - +
89A ILE* 1.3 79.7 - - - +
91A HIS* 1.3 70.2 + - - +
92A PRO* 3.3 7.3 - - - +
94A PHE* 5.4 2.5 - - - -
103A ILE 4.2 3.6 - - - -
104A ALA* 4.4 4.4 - - - +
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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