Contacts of the strand formed by residues 120 - 124 (chain S) in PDB entry 1I84
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 PHE 120 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116S TYR* 4.2 1.0 - - - +
117S SER* 3.0 61.2 + - - +
118S GLY 4.0 0.9 - - - +
119S LEU* 1.3 82.1 - - + +
121S CYS* 1.3 59.5 + - - +
122S VAL* 5.3 0.4 - - + -
493S PHE* 4.1 16.2 - + + -
497S MET* 4.5 7.9 - - - -
681S PHE* 3.6 34.8 - - + +
683S ARG* 3.3 31.0 - - + -
710S VAL* 3.4 43.1 - - + -
713S GLY* 3.0 33.2 - - - -
714S ILE* 4.0 0.2 - - + -
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Residues in contact with CYS 121 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S TYR* 4.8 3.8 - - - -
115S THR 3.2 17.0 - - - +
116S TYR* 3.5 22.4 - - + -
117S SER* 3.6 2.5 - - - -
119S LEU 5.0 0.9 - - - +
120S PHE* 1.3 79.4 - - - +
122S VAL* 1.3 71.4 + - - +
123S VAL* 3.7 9.9 - - - -
156S ILE* 3.5 32.5 - - + -
681S PHE 3.4 5.4 + - - +
682S VAL* 3.7 3.8 - - - -
683S ARG* 3.2 25.1 + - - -
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Residues in contact with VAL 122 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S MET* 5.2 3.1 - - + -
104S LEU* 4.5 28.0 - - + -
113S ILE 4.4 0.9 - - - -
115S THR* 2.8 30.9 + - - +
116S TYR 5.6 0.2 - - - -
117S SER* 3.4 22.2 - - - +
121S CYS* 1.3 69.7 - - - +
123S VAL* 1.3 82.4 + - - +
124S ILE* 4.6 6.7 - - + +
683S ARG* 3.8 11.0 - - + +
685S ILE* 3.5 35.4 - - + -
705S LEU* 4.4 5.8 - - + -
710S VAL* 4.6 15.9 - - + -
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Residues in contact with VAL 123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113S ILE* 3.6 12.8 - - + -
114S TYR* 3.7 39.5 - - + -
121S CYS* 3.7 13.2 - - - +
122S VAL* 1.3 93.1 - - - +
124S ILE* 1.3 62.7 + - - +
125S ASN* 3.2 3.9 + - - -
126S PRO* 6.4 0.7 - - + -
181S ALA 4.6 3.1 - - - +
186S ASN* 3.7 23.1 - - - +
682S VAL* 3.8 19.5 - - + +
683S ARG 3.6 4.9 + - - -
684S CYS* 4.2 10.7 - - - -
685S ILE 3.8 11.9 + - - -
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Residues in contact with ILE 124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S LEU* 3.9 50.0 - - + +
108S TYR* 3.7 26.9 - - + -
113S ILE* 3.1 35.9 + - + +
115S THR* 5.3 0.2 - - - +
122S VAL* 4.6 3.8 - - + -
123S VAL* 1.3 69.5 - - - +
125S ASN* 1.3 78.0 + - - +
126S PRO* 3.8 0.5 - - - +
685S ILE* 3.4 28.2 - - + +
687S PRO* 3.8 20.4 - - + -
696S LEU* 5.4 4.3 - - + -
701S VAL* 5.0 7.6 - - + -
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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
------------------------------------------------------------
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