Contacts of the strand formed by residues 198 - 203 (chain C) in PDB entry 1N34
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 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C ALA* 4.2 6.4 - - + +
120C VAL* 4.0 9.9 - - + -
121C ALA* 6.3 0.2 - - - +
124C ILE* 3.4 26.2 - - + +
151C VAL* 3.2 21.3 - - + -
152C ILE 2.8 36.8 - - - +
153C VAL* 3.2 34.1 - - + -
186C PHE* 3.0 19.3 - - - -
187C ALA* 3.0 17.5 + - - +
188C LEU 4.3 0.2 + - - -
197C GLY* 1.3 73.9 - - - -
199C LYS* 1.3 66.6 + - - +
200C ALA* 3.8 5.4 - - + +
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Residues in contact with LYS 199 (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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1058A G 3.0 36.1 + - - +
1059A C 3.0 30.2 + - - -
152C ILE* 3.9 20.5 + - + +
184C TYR* 3.7 25.4 - - + +
185C GLY 2.4 32.2 - - - +
186C PHE* 4.3 7.0 - - + -
198C VAL* 1.3 80.9 - - - +
200C ALA* 1.3 66.8 + - - +
201C TYR* 3.2 39.0 - - + +
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Residues in contact with ALA 200 (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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113C ALA* 3.3 26.6 - - + +
116C VAL* 4.7 5.2 - - + -
117C ALA* 4.1 21.3 - - + +
150C LYS 3.0 18.4 - - - +
151C VAL* 3.9 14.8 - - + +
184C TYR* 3.7 7.4 - - - -
185C GLY 3.5 2.4 - - - +
198C VAL* 3.8 7.3 - - + +
199C LYS* 1.3 91.2 - - - +
201C TYR* 1.3 65.6 + - - +
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Residues in contact with TYR 201 (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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4C LYS* 5.9 3.3 - - - +
5C ILE 6.1 0.2 - - - -
7C PRO* 4.6 15.4 - - + +
149C ALA* 3.3 21.5 - - - +
150C LYS* 3.4 37.9 + - + +
152C ILE* 4.0 14.3 - - + +
173C VAL* 5.0 3.8 - - + -
175C LEU* 3.3 36.6 - - + -
182C ILE* 5.2 4.3 - - + -
183C ASP 3.7 8.5 - - - +
184C TYR* 4.0 18.5 - + - +
199C LYS* 3.2 44.8 - - + +
200C ALA* 1.3 80.5 - - - +
202C ILE* 1.3 75.3 + - - +
203C PHE 5.5 0.2 - - - +
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Residues in contact with ILE 202 (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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111C LEU* 3.9 3.4 - - - +
112C SER 3.8 10.1 - - - +
113C ALA* 3.0 41.3 - - + +
116C VAL* 3.9 6.7 - - + -
141C VAL* 3.8 28.0 - - + -
148C GLY 3.7 9.0 - - - +
149C ALA* 5.0 0.4 - - + -
182C ILE* 3.4 2.0 - - - -
183C ASP* 2.6 48.8 + - - +
201C TYR* 1.3 87.6 - - - +
203C PHE* 1.3 60.0 + - - +
204C LEU* 3.2 35.7 - - + +
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Residues in contact with PHE 203 (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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147C LYS* 3.1 43.7 + - + -
148C GLY 3.3 23.9 + - - +
149C ALA 4.4 0.4 + - - +
172C ARG* 3.5 47.3 - - + +
173C VAL* 4.7 2.7 - - + -
174C PRO* 4.0 11.9 - - + -
180C ALA* 3.2 23.6 - - + -
182C ILE* 3.3 27.0 - - + +
201C TYR* 5.5 0.4 - - - +
202C ILE* 1.3 73.0 - - - +
204C LEU* 1.3 99.4 + - - +
205C GLY 3.2 7.6 - - - -
206C GLU* 2.9 27.4 - - - -
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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