Contacts of the strand formed by residues 158 - 161 (chain I) in PDB entry 1CL7
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 158 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156I PRO* 4.3 9.4 - - + -
157I VAL* 1.3 72.6 - - - +
159I VAL* 1.3 59.7 + - - +
160I THR* 3.7 5.2 + - - -
203I ASN 2.8 7.6 - - - +
204I VAL* 3.0 0.2 - - - -
205I ALA* 2.7 60.7 + - - +
207I PRO* 5.1 6.0 - - + +
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Residues in contact with VAL 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I CYS* 4.7 1.6 - - + -
149I VAL* 4.1 10.8 - - + -
157I VAL* 3.2 7.9 + - + +
158I THR* 1.3 73.2 - - - +
160I THR* 1.3 62.4 + - - +
161I TRP* 3.9 9.1 - - - +
170I VAL* 5.3 3.3 - - - +
172I THR* 3.5 27.2 + - + +
184I LEU* 3.5 31.4 - - + -
186I SER* 3.4 24.2 - - - +
202I CYS* 3.9 26.5 - - - -
203I ASN 3.1 2.7 - - - -
204I VAL* 4.2 6.7 - - + -
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Residues in contact with THR 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I THR* 5.1 5.2 + - - -
159I VAL* 1.3 76.3 + - - +
161I TRP* 1.3 72.3 + - - +
163I SER* 3.5 5.4 - - - -
164I GLY* 2.9 35.0 - - - +
170I VAL* 6.1 0.7 - - - -
202I CYS* 3.8 0.5 - - - -
203I ASN* 2.7 54.0 + - + +
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Residues in contact with TRP 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I LEU* 4.4 4.0 - - + -
146I GLY* 3.2 31.6 - - - -
147I CYS* 3.7 15.0 - - + -
159I VAL* 3.9 5.5 - - + +
160I THR* 1.3 84.5 - - - +
162I ASN* 1.3 72.7 + - - +
163I SER 3.3 1.1 - - - -
164I GLY* 3.2 8.9 + - - -
166I LEU* 3.2 37.9 + - + +
170I VAL* 3.8 23.5 - - + +
186I SER* 2.7 46.2 + - - -
187I SER* 4.2 6.5 + - - -
188I VAL* 3.5 27.4 - - + -
200I VAL* 4.6 6.5 - - + -
201I THR 3.5 17.5 - - - -
202I CYS* 3.9 4.0 - - + -
203I ASN* 3.2 1.6 - - - -
217I ILE* 3.8 23.6 - - + -
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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
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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