Contacts of the strand formed by residues 96 - 104 (chain A) in PDB entry 5D4C
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 THR 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.3 1.5 - - - -
94A LEU* 3.4 14.7 - - + +
95A GLN* 1.3 86.9 - - + +
97A VAL* 1.3 74.4 + - - +
98A THR* 4.9 1.9 + - - -
143A ARG* 3.9 23.8 + - - +
144A VAL 3.4 9.2 + - - -
145A ASP* 3.3 17.8 + - - +
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Residues in contact with VAL 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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89A PHE* 3.5 30.1 - - + -
94A LEU* 3.6 21.8 - - + -
96A THR* 1.3 84.5 + - - +
98A THR* 1.3 69.8 + - - +
99A LEU* 3.5 24.1 + - + -
117A VAL* 4.4 15.3 - - + -
120A VAL* 3.6 18.4 - - + -
142A VAL 3.6 1.6 - - - +
143A ARG* 3.7 0.9 - - - -
144A VAL* 2.9 32.2 + - + +
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Residues in contact with THR 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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96A THR* 4.9 2.1 + - - -
97A VAL* 1.3 80.6 + - - +
99A LEU* 1.3 62.6 + - - +
100A LEU* 3.8 28.1 + - + +
117A VAL* 4.7 7.4 - - - +
141A GLU* 4.1 17.7 - - + +
142A VAL 3.4 11.7 - - - +
143A ARG* 4.4 8.2 - - + +
160A ASP* 3.9 18.1 + - - +
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Residues in contact with LEU 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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85A LEU* 4.2 15.3 - - + -
87A VAL* 4.6 5.8 - - + -
97A VAL* 3.5 24.9 - - + -
98A THR* 1.3 73.3 - - - +
100A LEU* 1.3 61.0 + - - +
101A LEU 4.3 0.2 + - - -
114A PHE* 3.6 35.4 - - + -
115A LEU 5.2 6.1 - - - +
117A VAL* 5.2 4.9 - - + -
120A VAL* 4.6 10.3 - - + -
122A ILE* 3.8 25.1 - - + -
140A MET 4.0 0.2 - - - +
141A GLU* 3.4 4.2 - - - -
142A VAL* 2.9 45.0 + - + +
144A VAL* 4.1 21.1 - - + -
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Residues in contact with LEU 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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98A THR* 3.9 21.1 - - + +
99A LEU* 1.3 82.9 - - - +
101A LEU* 1.3 62.3 + - - +
102A LYS* 6.1 4.5 - - - -
114A PHE* 3.5 3.4 - - - -
115A LEU* 2.9 54.2 + - + +
117A VAL* 6.4 0.9 - - + -
139A ASN* 5.9 1.3 - - - +
140A MET 3.5 4.7 - - - +
141A GLU* 3.7 26.2 - - + -
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Residues in contact with LEU 101 (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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99A LEU 4.3 0.2 - - - -
100A LEU* 1.3 76.1 - - - +
102A LYS* 1.3 61.3 + - - +
103A ALA* 3.9 17.3 - - + -
109A VAL* 3.6 35.0 - - + -
110A LYS 4.0 5.2 - - - +
113A ASP* 4.1 12.3 - - + +
114A PHE* 3.7 30.7 - - + +
129A ILE* 3.7 22.2 - - + -
138A LEU* 3.3 15.2 - - + +
139A ASN* 3.3 4.9 - - - +
140A MET* 2.9 55.6 + - + -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.2 5.3 - - - -
101A LEU* 1.3 73.5 - - - +
103A ALA* 1.3 62.6 + - - +
113A ASP* 4.9 6.0 + - - +
115A LEU* 5.4 18.3 - - + +
138A LEU 3.6 2.0 - - - +
139A ASN* 3.6 34.2 - - + +
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Residues in contact with ALA 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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101A LEU* 3.9 12.1 - - + -
102A LYS* 1.3 76.9 - - - +
104A GLU* 1.3 68.7 + - - +
107A LYS* 4.4 13.7 - - + +
109A VAL* 3.7 30.7 - - + -
113A ASP* 5.4 3.4 - - + -
132A LEU* 3.8 3.8 - - + -
137A ARG* 3.7 1.4 - - - +
138A LEU 2.9 31.7 + - - +
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Residues in contact with GLU 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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103A ALA* 1.3 81.3 - - - +
105A GLY* 1.3 71.7 + - - +
106A PRO 4.8 0.2 - - - +
107A LYS* 3.4 16.9 - - - +
132A LEU* 3.8 3.1 - - - +
136A GLY 3.3 14.8 - - - +
137A ARG* 4.0 21.9 + - + +
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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