Contacts of the strand formed by residues 118 - 120 (chain O) in PDB entry 2GLJ
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 LEU 118 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O ASN* 3.5 5.3 - - - +
117O PRO* 1.3 80.1 - - - +
119O TYR* 1.3 67.2 + - - +
125O ALA* 4.7 2.7 - - + -
126O MET 3.8 4.9 - - - +
127O LEU* 3.5 7.0 - - + -
201O ILE* 3.6 32.5 - - + -
218O LYS* 3.4 43.8 + - + -
221O ILE* 3.6 22.0 - - + -
222O MET* 3.7 32.3 - - + -
225O LEU* 5.8 2.0 - - + -
233O GLU* 3.6 15.2 + - + +
236O PHE* 4.4 15.3 - - + -
358P ARG* 5.3 2.4 - - - -
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Residues in contact with TYR 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O PRO 3.3 19.6 + - - -
118O LEU* 1.3 77.7 - - - +
120O GLU* 1.3 68.0 + - - +
121O ASP* 3.7 23.9 - - + +
125O ALA* 3.4 5.6 - - - +
126O MET* 3.0 60.8 + - + +
127O LEU 4.3 0.4 - - - -
128O GLU* 3.0 39.0 - - + -
197O GLU* 2.9 26.5 + - + +
215O GLN* 4.8 2.0 - - - +
218O LYS* 4.2 10.8 - - - +
358P ARG* 3.7 36.8 - - - +
349R PRO 5.5 2.1 + - - -
350R ASN* 4.8 0.5 + - - -
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Residues in contact with GLU 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O TYR* 1.3 79.3 - - - +
121O ASP* 1.3 59.3 + - - +
122O THR 4.3 1.0 + - - -
123O ASP* 2.9 33.9 + - - +
124O LEU 3.3 8.1 - - - +
125O ALA* 3.9 4.7 - - + +
214O LYS 4.0 4.5 - - - +
215O GLN* 3.2 39.0 + - - +
216O LYS 3.2 5.1 + - - -
217O VAL* 2.6 33.2 + - - +
218O LYS* 2.7 21.9 + - + -
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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
------------------------------------------------------------
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