Contacts of the strand formed by residues 90 - 96 (chain A) in PDB entry 3KSS
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 ASP 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LYS* 4.6 3.8 - - - -
51A THR 3.6 5.5 - - - +
52A SER* 4.2 17.1 + - - -
53A TYR* 4.5 1.3 - - - +
61A VAL* 3.0 7.3 - - - +
85A PHE 4.2 0.4 - - - +
86A SER 3.8 0.3 - - - -
87A GLN* 2.9 36.8 + - - +
88A PHE 3.2 5.6 + - - +
89A GLY* 1.3 98.7 - - - +
91A SER* 1.3 62.0 + - - +
92A TYR* 3.7 20.1 + - + -
611A LYS* 3.1 36.7 + - - +
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Residues in contact with SER 91 (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 ILE 3.2 6.2 - - - +
51A THR* 2.8 36.1 + - - -
61A VAL* 4.0 4.0 - - - -
65A VAL* 3.8 20.4 - - - +
66A THR* 3.0 42.9 - - - -
69A LEU* 4.4 0.9 - - - +
85A PHE 3.7 4.7 + - - -
86A SER* 4.4 0.7 - - - +
90A ASP* 1.3 74.8 - - - +
92A TYR* 1.3 60.5 + - - +
93A VAL* 3.8 6.9 + - - +
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Residues in contact with TYR 92 (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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48A ILE* 4.7 4.5 - - + -
49A ILE 3.9 0.9 - - - -
50A LYS* 3.2 54.7 - - + +
51A THR 5.1 0.2 - - - -
84A GLY* 3.3 1.0 - - - -
85A PHE* 2.5 50.0 + - + +
87A GLN* 4.5 10.1 - - - -
90A ASP* 3.7 15.0 + - + -
91A SER* 1.3 73.6 - - - +
93A VAL* 1.3 58.9 + - - +
94A TYR* 4.2 20.6 + - + +
611A LYS* 3.2 37.5 + - - +
614A THR 4.4 0.9 + - - -
615A ALA 3.7 18.6 - - - -
617A ASP 3.3 17.6 + - - -
618A SER* 3.4 23.3 - - - -
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Residues in contact with VAL 93 (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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47A VAL 3.5 4.0 - - - +
48A ILE* 5.5 0.4 - - - +
49A ILE* 3.0 57.4 + - + +
66A THR* 4.3 3.6 - - - -
69A LEU* 4.0 18.4 - - + +
70A THR* 3.9 35.0 - - + +
73A MET* 5.3 1.3 - - + -
82A VAL* 4.7 11.0 - - + -
84A GLY* 3.7 8.7 - - - -
85A PHE 6.0 0.4 - - - -
91A SER* 4.0 16.2 - - - +
92A TYR* 1.3 76.0 - - - +
94A TYR* 1.3 71.2 + - - +
95A VAL* 4.8 2.9 - - + -
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Residues in contact with TYR 94 (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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46A GLN* 4.0 18.8 - - + +
47A VAL 3.7 2.2 - - - +
48A ILE* 3.9 37.1 - - + +
81A THR 3.8 1.4 - - - +
82A VAL* 3.9 2.6 - - - -
83A ARG 3.3 40.0 + - - +
84A GLY* 4.9 0.4 - - - -
85A PHE* 4.0 30.9 - + - -
92A TYR* 4.3 20.4 - - + +
93A VAL* 1.3 74.3 - - - +
95A VAL* 1.3 65.0 + - - +
96A ILE* 4.1 16.5 - - + +
615A ALA 5.4 0.3 + - - -
616A THR 4.6 6.5 + - - -
618A SER* 3.6 23.7 + - - -
672A MET 4.7 2.9 + - - -
673A LEU* 4.4 24.2 - - + +
675A THR* 4.3 13.0 - - + -
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Residues in contact with VAL 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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46A GLN* 3.1 7.1 - - - -
47A VAL* 3.0 42.6 + - + +
49A ILE* 4.6 10.5 - - + -
73A MET* 4.7 11.4 - - + -
76A VAL* 4.9 3.1 - - + -
79A ALA* 4.4 15.7 - - + -
81A THR 3.9 5.2 - - - +
82A VAL* 4.7 12.3 - - + -
93A VAL* 4.8 3.4 - - + -
94A TYR* 1.3 77.6 - - - +
96A ILE* 1.3 66.5 + - - +
97A PHE* 3.9 30.1 + - + -
110A VAL* 4.4 19.5 - - + -
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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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44A ASP* 3.7 28.5 - - - +
45A VAL 3.8 2.2 - - - +
46A GLN* 4.6 7.4 - - - +
80A LYS* 3.0 54.9 + - - +
81A THR* 3.0 33.2 + - - +
83A ARG* 4.7 3.8 - - + -
94A TYR* 4.1 13.2 - - + +
95A VAL* 1.3 78.0 - - - +
97A PHE* 1.3 66.3 + - - +
675A THR* 3.7 30.3 - - + +
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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