Contacts of the strand formed by residues 115 - 119 (chain C) in PDB entry 3B94
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 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C VAL* 4.4 20.6 - - + +
113C PHE* 4.4 15.0 - - + -
114C GLU* 1.3 76.9 - - - +
116C ARG* 1.3 65.8 + - - +
125C GLN 3.8 0.2 - - - +
126C THR* 3.1 7.6 + - - -
127C LEU* 2.8 46.1 + - + +
136C VAL* 5.3 3.4 - - + -
150C LEU* 3.4 37.0 - - + -
151C ILE 3.6 7.4 - - - +
152C PHE* 3.6 27.8 - - + -
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Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLU* 2.9 39.3 + - - +
115C VAL* 1.3 80.1 - - - +
117C LEU* 1.3 60.6 + - - +
118C TYR* 3.6 27.0 + - + -
123C MET* 3.5 24.9 - - - +
125C GLN 3.3 9.6 - - - +
126C THR* 4.5 0.2 - - - -
149C ASP 3.4 2.3 - - - +
150C LEU* 3.2 9.7 - - - -
151C ILE* 2.7 72.5 + - + +
153C ASN* 4.7 13.7 - - - +
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ILE* 4.0 16.2 - - + -
116C ARG* 1.3 74.3 - - - +
118C TYR* 1.3 59.8 + - - +
123C MET* 3.6 6.9 - - - +
124C ILE* 3.0 41.4 + - + -
125C GLN* 2.9 23.3 + - + +
136C VAL* 4.9 4.0 - - + -
137C GLY* 3.7 33.9 - - - +
140C TYR* 4.0 13.9 - - - +
148C ILE* 3.4 29.4 - - + -
149C ASP 3.5 10.3 - - - +
150C LEU* 3.9 15.6 - - + +
165C TRP* 4.9 5.6 - - + -
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Residues in contact with TYR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ARG* 3.6 40.3 + - + -
117C LEU* 1.3 79.6 - - - +
119C LYS* 1.4 56.4 + - - +
120C ASN 4.0 9.4 - - - +
121C LYS* 3.6 22.2 - - - -
122C ASP 3.3 19.5 - - - -
123C MET* 3.8 17.8 - - + +
124C ILE* 4.3 4.7 - - - +
147C THR 4.2 0.2 - - - -
148C ILE* 3.0 31.1 - - - +
149C ASP* 2.9 23.2 + - - +
151C ILE* 3.3 35.9 - - + +
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLN* 5.2 16.2 - - - +
164B TYR* 6.1 0.9 - - - -
118C TYR* 1.4 70.3 - - - +
120C ASN* 1.3 84.4 + - - +
122C ASP* 2.9 32.4 + - + +
124C ILE* 4.1 24.6 - - + +
140C TYR* 5.8 3.6 - - + -
141C GLU 3.8 17.4 + - - +
142C LEU* 3.7 23.1 - - + +
143C HIS* 4.4 10.3 - - - +
146C ASP* 2.6 32.9 + - + +
147C THR 3.1 8.3 - - - +
148C ILE* 4.4 4.9 - - + -
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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