Contacts of the strand formed by residues 119 - 122 (chain C) in PDB entry 1ESQ
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 ALA 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C VAL 3.7 3.4 + - - +
92C ILE* 3.6 19.5 - - + +
93C LEU 3.1 22.0 + - - -
117C LEU* 3.3 2.8 - - - +
118C ALA* 1.3 83.9 - - + +
120C ILE* 1.3 69.6 + - - +
121C ARG* 6.4 0.4 - - + -
163C THR* 3.6 1.8 - - - -
164C VAL* 3.1 25.8 - - + +
166C ALA* 6.0 2.0 - - + -
204C VAL* 4.7 12.6 - - + -
208C CYS* 5.1 2.0 - - - -
214C PRO* 5.0 4.5 - - + -
218C ALA* 5.2 3.6 - - + -
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Residues in contact with ILE 120 (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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93C LEU* 3.2 17.7 - - + +
95C PRO* 3.6 21.8 - - + -
112C ILE* 4.1 8.1 - - + -
117C LEU* 3.9 26.5 - - + -
119C ALA* 1.3 82.7 - - - +
121C ARG* 1.3 62.3 + - - +
127C ILE* 4.0 16.0 - - + +
130C THR* 5.1 4.5 - - + -
131C VAL* 5.9 0.2 - - + -
161C LEU* 3.8 28.5 - - + -
163C THR* 4.0 16.2 - - + -
164C VAL 2.8 10.2 + - - +
165C ILE* 3.8 9.3 - - + -
166C ALA* 3.0 26.5 + - - +
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Residues in contact with ARG 121 (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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92C ILE* 5.2 2.6 - - + +
93C LEU 2.9 7.8 + - - +
94C ASP* 3.1 39.3 + - - +
95C PRO* 3.1 19.3 - - - +
119C ALA* 6.4 0.2 - - + -
120C ILE* 1.3 74.6 - - - +
122C GLY* 1.3 80.3 + - - +
127C ILE* 4.6 1.1 - - - -
166C ALA* 3.4 20.9 - - + +
168C THR* 2.6 36.9 + - + -
197C GLY* 3.3 17.1 + - - -
200C LEU* 3.7 28.9 - - - -
201C THR* 2.7 31.8 + - + +
204C VAL* 4.9 8.5 - - + -
222C ILE* 5.1 2.0 - - + -
310C ATP 2.8 31.2 + - - -
350C MG 3.2 3.4 - - - -
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Residues in contact with GLY 122 (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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94C ASP* 4.6 0.4 - - - -
95C PRO* 4.6 4.7 - - - -
121C ARG* 1.3 96.1 - - - +
123C ASN* 1.3 67.3 + - - +
126C GLU* 3.4 11.7 - - - -
127C ILE* 3.9 9.3 - - - +
166C ALA 3.3 2.7 + - - +
167C ILE* 3.4 21.7 - - - -
168C THR 3.4 4.7 + - - -
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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