Contacts of the strand formed by residues 122 - 126 (chain C) in PDB entry 5H1C
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 ILE 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C SER* 1.3 74.7 - - - +
123C THR* 1.3 64.6 + - - +
249C LEU* 4.3 10.3 - - + +
252C LEU* 4.0 24.5 - - + +
253C LEU* 3.9 31.4 - - + -
256C ALA* 5.2 0.4 - - + -
263C VAL* 3.6 16.8 - - + -
265C ILE* 2.9 36.8 - - + -
295C ALA* 5.0 10.3 - - + +
296C SER* 4.2 21.6 - - - +
297C THR* 2.8 28.3 + - + +
298C THR* 3.2 12.1 + - - -
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Residues in contact with THR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 3.7 36.9 - - + +
118C GLU 5.5 0.7 - - - +
121C SER* 5.1 5.6 - - - +
122C ILE* 1.3 77.6 - - - +
124C GLU* 1.3 64.2 + - - +
125C MET* 5.6 2.2 - - - -
263C VAL 2.9 19.8 + - - +
264C VAL* 3.2 22.6 - - - +
265C ILE* 2.8 31.8 + - - +
298C THR* 3.2 25.4 - - + +
300C LEU* 5.8 4.7 - - - -
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Residues in contact with GLU 124 (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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123C THR* 1.3 78.3 - - - +
125C MET* 1.3 66.9 + - - +
126C PHE* 3.8 2.9 - - + -
265C ILE* 3.1 9.4 + - - +
267C ASN* 2.5 40.9 + - - +
292C ILE* 2.7 22.4 - - - +
296C SER* 3.0 24.5 - - - -
298C THR* 4.3 2.4 + - - -
299C ARG* 2.5 54.8 + - - +
300C LEU* 2.9 35.7 + - - +
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Residues in contact with MET 125 (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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117C ILE* 5.3 5.8 - - + -
123C THR* 5.4 1.1 - - - +
124C GLU* 1.3 86.7 - - - +
126C PHE* 1.3 65.9 + - - +
127C GLY 4.0 0.2 - - - -
133C LYS* 3.8 21.2 - - + +
136C ILE* 4.0 36.6 - - + -
137C CYS* 5.1 1.8 - - - -
140C LEU* 5.2 2.7 - - + -
264C VAL* 4.3 20.2 - - + -
265C ILE 2.8 14.8 + - - +
266C THR* 3.2 34.5 - - + +
267C ASN* 3.1 26.7 + - - +
300C LEU* 4.2 20.0 - - + -
302C LEU* 4.8 7.0 - - + -
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Residues in contact with PHE 126 (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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129B PHE* 5.9 2.5 - + - -
130B ARG* 6.2 1.1 - - - -
124C GLU* 3.8 8.5 - - + -
125C MET* 1.3 80.6 - - - +
127C GLY* 1.3 56.5 + - - +
133C LYS* 5.5 0.2 - - - -
267C ASN* 4.2 2.2 - - + -
269C VAL* 5.2 4.9 - - + -
284C LYS* 6.1 0.2 - - + -
285C LYS* 4.5 3.8 - - - -
286C PRO* 2.3 61.2 - - + -
299C ARG* 2.7 37.7 - - - -
300C LEU 2.8 25.1 + - - +
301C TYR* 3.3 28.5 - + + -
302C LEU* 2.6 38.3 + - - +
315C TYR* 4.1 19.7 - + - -
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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