Contacts of the strand formed by residues 114 - 117 (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 TYR 114 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LEU* 4.9 2.2 - - + +
107S ARG* 3.1 18.0 + - - -
112S LEU* 4.9 2.3 - - - +
113S ILE* 1.3 93.7 + - + +
115S THR* 1.3 62.6 + - - +
121S CYS* 4.8 7.2 - - - -
122S VAL 3.7 5.2 - - - +
123S VAL* 3.7 20.6 - - + +
132S ILE* 3.8 19.1 - - + -
133S TYR* 2.5 36.8 + - - -
151S PRO* 3.5 31.5 - - + +
152S HIS* 3.7 8.1 - - - +
153S ILE* 3.1 44.6 - - + +
156S ILE* 4.9 0.4 - - + -
186S ASN* 3.4 27.9 + - - -
189S LYS* 4.9 1.4 - - - +
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Residues in contact with THR 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S VAL 4.0 3.4 - - - +
87S GLU 3.8 8.1 - - - +
89S MET* 4.3 5.6 - - - -
103S ASN* 4.2 4.9 - - - +
104S LEU* 3.9 28.3 - - + +
107S ARG* 3.4 37.4 + - - +
113S ILE 3.4 9.7 + - - -
114S TYR* 1.3 76.9 + - - +
116S TYR* 1.3 73.5 + - - +
121S CYS* 3.2 4.9 - - - +
122S VAL* 2.8 38.0 + - - +
124S ILE* 5.3 0.7 - - - +
151S PRO* 4.0 3.1 - - - +
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Residues in contact with TYR 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S GLU* 3.0 19.3 + - + +
88S ASP* 3.4 20.3 - - + -
89S MET* 3.1 31.2 + - - +
115S THR* 1.3 76.1 - - - +
117S SER* 1.3 60.3 + - - +
118S GLY 4.7 6.1 - - - +
119S LEU 5.8 1.8 - - - -
120S PHE 4.7 1.3 - - - +
121S CYS* 3.5 25.8 - - + -
122S VAL* 5.6 0.2 - - - -
146S ARG* 4.3 27.3 + - + -
150S PRO 4.6 0.5 + - - -
151S PRO* 3.5 36.0 - - + +
152S HIS 4.5 2.9 - - - -
155S ALA* 3.4 26.9 - - - +
156S ILE* 4.9 8.8 + - + -
159S THR* 5.5 1.4 + - - -
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Residues in contact with SER 117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88S ASP* 4.0 2.0 - - - -
89S MET* 4.2 6.3 - - - -
116S TYR* 1.3 72.3 - - - +
118S GLY* 1.3 61.6 + - - +
120S PHE* 3.0 57.5 + - - +
121S CYS* 3.6 2.1 - - - -
122S VAL* 3.4 27.5 - - - +
710S VAL* 4.4 0.9 - - - -
714S ILE* 3.4 32.5 - - - -
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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