Contacts of the strand formed by residues 94 - 100 (chain A) in PDB entry 3DJI
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 VAL 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.7 1.1 - - - -
57A ALA* 3.4 14.8 - - + +
59A CYS* 4.2 2.2 - - - -
80A CYS* 4.2 15.0 - - - +
83A LEU* 3.9 27.4 - - + -
89A ILE* 3.5 27.6 - - + +
90A SER 3.7 6.1 - - - +
91A PRO* 3.4 12.3 + - + +
92A ASP 3.5 0.6 - - - -
93A ARG* 1.3 85.0 - - - +
95A TYR* 1.3 73.2 + - - +
96A ILE* 4.0 14.4 - - + -
108B TRP* 3.2 30.5 - - - -
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Residues in contact with TYR 95 (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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49A PHE* 3.4 30.6 - + - -
57A ALA 3.1 6.3 + - - +
58A LEU* 3.6 16.3 - - + -
59A CYS* 2.8 32.3 + - - +
94A VAL* 1.3 79.7 - - - +
96A ILE* 1.3 59.9 + - - +
97A ASN 4.2 0.4 - - - -
1B PRO 4.0 11.4 - - - -
2B MET* 3.8 27.1 - - + -
36B TYR* 2.7 41.5 + - - +
38B ALA* 4.1 6.1 - - + -
106B VAL* 4.4 8.7 - - + -
107B GLY 3.2 9.9 - - - -
108B TRP* 3.6 24.9 + + + -
113B PHE* 4.0 13.1 - + - -
201B 3E1 3.5 17.1 - - + +
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Residues in contact with ILE 96 (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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3A PHE* 4.6 6.5 - - + -
59A CYS* 3.2 25.8 - - + +
60A SER 4.6 0.2 - - - +
61A LEU* 4.5 6.1 - - + +
76A SER* 4.4 5.4 - - - +
79A LEU* 3.8 30.3 - - + -
80A CYS* 4.3 13.5 - - - -
83A LEU* 5.2 0.9 - - + -
94A VAL* 4.0 16.6 - - + -
95A TYR* 1.3 80.2 - - - +
97A ASN* 1.3 68.7 + - - +
98A TYR* 3.5 38.7 - - + +
106B VAL* 3.4 3.0 - - - +
107B GLY* 2.6 39.9 + - - +
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Residues in contact with ASN 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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59A CYS 2.8 12.6 + - - +
60A SER* 3.4 5.5 + - - +
61A LEU 3.0 23.9 + - - -
96A ILE* 1.3 75.3 - - - +
98A TYR* 1.3 61.1 + - - +
99A TYR* 3.5 24.4 + - + +
2B MET* 3.3 37.1 - - - +
62B HIS* 3.4 27.1 + - - +
101B MET* 3.7 20.0 - - + +
105B ASN 3.5 2.2 - - - -
106B VAL* 3.7 16.5 - - - +
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Residues in contact with TYR 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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61A LEU* 3.6 28.3 - - + -
67A ILE* 4.3 8.7 - - + -
72A ASN* 3.6 41.7 - - + +
75A TYR* 3.3 24.0 - + + +
76A SER* 2.8 47.3 + - - -
79A LEU* 4.3 1.5 - - + +
96A ILE* 3.5 37.5 - - + +
97A ASN* 1.3 73.0 - - - +
99A TYR* 1.3 67.3 + - - +
101B MET* 4.1 5.2 - - - +
105B ASN* 2.8 48.3 + - + +
106B VAL 4.6 0.4 - - - -
107B GLY* 3.7 5.8 - - - -
112B THR* 5.0 0.2 - - + -
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Residues in contact with TYR 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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60A SER* 4.2 7.3 + - - -
61A LEU 3.0 9.3 + - - -
62A HIS* 3.4 48.6 - + + -
63A SER 3.0 26.0 + - - +
67A ILE* 3.7 7.3 - - - +
97A ASN* 3.5 34.9 + - + +
98A TYR* 1.3 77.9 - - - +
100A ASP* 1.3 60.7 + - - +
101A MET* 3.5 7.1 + - - -
62B HIS* 2.9 33.3 + - - -
99B TYR* 4.8 15.4 - + - -
101B MET* 4.3 14.1 - - + -
99C TYR* 4.9 12.1 - + - -
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Residues in contact with ASP 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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63A SER 3.4 3.1 - - - -
65A GLY* 3.1 27.9 + - - -
67A ILE* 3.6 37.6 - - + +
99A TYR* 1.3 70.3 - - - +
101A MET* 1.3 66.5 + - - +
102A ASN* 4.0 4.0 + - - +
602A CL 4.2 6.8 - - - +
105B ASN* 6.0 1.2 - - - +
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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