Contacts of the strand formed by residues 123 - 126 (chain B) in PDB entry 1ZVM
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 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B LYS 3.7 0.2 + - - -
122B ILE* 1.3 76.1 - - - +
124B LEU* 1.3 72.6 + - - +
125B TRP* 4.2 1.4 - - + -
132B ALA* 4.3 19.1 - - + +
135B PHE* 4.4 12.3 - - + -
136B THR* 4.8 1.6 - - + -
142B MET* 4.0 19.5 - - + -
143B PHE 2.8 17.3 + - - +
144B THR* 3.4 35.2 - - + +
145B LEU 4.9 0.2 + - - -
205B HIS* 3.3 33.4 - - + -
206B VAL 4.0 1.3 - - - +
207B MET* 4.4 11.7 - - + +
241B TRP* 4.1 17.9 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 3.8 10.3 - - + -
123B LEU* 1.3 80.3 - - - +
125B TRP* 1.3 63.0 + - - +
145B LEU 6.2 0.2 - - - +
196B PHE* 3.6 36.1 - - + -
197B ALA* 5.2 6.5 - - + -
204B VAL* 4.0 17.5 - - + -
205B HIS 2.7 15.2 + - - +
206B VAL* 3.1 11.6 - - + -
207B MET 2.9 20.6 + - - -
222B PHE* 3.8 18.6 - - + -
226B GLU* 3.1 35.4 - - + +
230B LEU* 4.5 15.9 - - + -
238B LEU* 5.1 0.7 - - + -
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Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU 4.2 9.0 - - - -
124B LEU* 1.3 81.8 - - - +
126B SER* 1.3 62.6 + - - +
127B ARG* 3.5 17.0 - - - -
128B ILE* 3.5 22.2 - - + -
129B LYS* 3.4 46.9 - - + -
132B ALA* 3.9 26.7 - - + -
133B HIS* 4.4 1.2 - - - -
144B THR* 4.2 9.3 - - - -
145B LEU* 5.0 3.7 - - - +
146B GLU* 2.8 37.6 + - - -
206B VAL* 4.1 3.6 - - - -
207B MET* 3.5 14.1 - - + +
222B PHE* 4.4 1.7 - - - +
226B GLU* 4.2 15.0 + - - +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TRP* 1.3 78.7 - - - +
127B ARG* 1.3 83.9 + - - +
128B ILE* 3.2 9.4 + - - +
207B MET 3.2 6.9 + - - +
208B LEU* 3.7 21.4 - - - -
209B ASP* 4.2 8.8 + - - +
215B ILE 5.5 2.4 + - - +
216B PHE* 6.5 0.4 - - - -
217B ASP* 5.6 2.3 + - - +
220B SER* 3.6 20.8 + - - -
222B PHE* 3.9 15.7 + - - +
303B SO4 4.8 3.0 + - - -
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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