Contacts of the strand formed by residues 215 - 220 (chain B) in PDB entry 4H1S
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 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY* 3.4 6.3 - - - +
174B VAL* 4.1 21.1 - - + -
204B VAL* 4.6 15.0 - - + +
207B LEU* 3.7 35.2 - - + -
208B LYS* 4.5 10.3 - - - +
212B VAL* 3.8 22.2 - - + +
214B LYS* 1.3 82.2 - - - +
216B ILE* 1.3 69.9 + - - +
235B GLY 3.5 23.6 - - - +
236B VAL* 3.9 8.7 - - + -
237B ASP* 2.7 43.5 + - - +
238B VAL 3.5 2.6 + - - -
294B PHE* 5.4 0.4 - - - -
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Residues in contact with ILE 216 (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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29B LEU* 4.1 9.9 - - + -
31B ILE* 3.6 27.1 - - + -
79B LEU* 4.2 8.3 - - + -
81B LEU* 4.2 21.1 - - + -
171B VAL* 3.8 22.9 - - + -
172B GLY 2.7 12.0 + - - +
173B ILE* 3.2 10.2 - - + -
174B VAL* 2.9 25.1 + - - -
215B ILE* 1.3 79.8 - - - +
217B ALA* 1.3 72.0 + - - +
218B LEU* 3.7 4.3 + - + +
238B VAL* 3.6 16.2 - - + +
240B VAL* 4.0 19.5 - - + -
294B PHE* 6.0 3.4 - - + -
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 3.4 9.2 - - + +
176B TYR* 3.9 17.9 - - + -
200B LEU* 5.1 5.8 - - + -
215B ILE* 4.1 1.6 + - - +
216B ILE* 1.3 71.8 - - - +
218B LEU* 1.3 55.6 + - - +
229B ILE* 4.1 15.0 - - + -
236B VAL* 4.0 26.5 - - + +
238B VAL 3.0 7.6 + - - +
239B VAL* 3.4 4.8 - - + +
240B VAL 2.8 32.1 + - - +
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Residues in contact with LEU 218 (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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81B LEU* 3.9 24.2 - - + -
82B ASP 3.6 27.6 - - - +
83B ALA* 3.9 7.6 - - + -
112B ALA* 4.1 14.8 - - + +
113B MET 4.2 1.3 - - - -
114B ALA* 3.3 16.9 - - + +
140B LEU* 5.0 1.8 - - + -
173B ILE* 3.7 28.9 - - + -
174B VAL 2.8 8.6 + - - +
175B GLY* 3.0 25.7 - - - -
176B TYR* 3.2 2.8 + - - -
216B ILE* 3.7 4.2 + - + -
217B ALA* 1.3 72.7 - - - +
219B GLY* 1.3 58.4 + - - +
240B VAL* 3.4 35.2 - - + +
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Residues in contact with GLY 219 (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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83B ALA* 3.7 7.4 - - - +
114B ALA* 3.8 6.1 - - - -
176B TYR* 3.1 32.4 + - - -
218B LEU* 1.3 78.5 - - - +
220B HIS* 1.3 60.4 + - - -
221B SER 4.0 0.2 + - - -
240B VAL 3.0 8.3 + - - -
241B GLY* 3.3 26.0 - - - -
242B GLY 3.5 2.9 + - - -
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Residues in contact with HIS 220 (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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36B ASP* 3.2 26.9 - - - -
83B ALA 2.8 24.8 + - - +
84B GLY 3.8 2.0 - - - -
85B ASP* 2.9 17.2 + - + -
114B ALA* 5.5 0.2 - - + -
115B LEU 3.6 20.6 - - - +
116B GLY* 3.5 11.7 - - - -
117B ASN* 3.1 12.8 - - - -
176B TYR* 2.9 10.1 + - - +
177B THR* 4.6 0.4 - - - -
178B SER* 2.9 20.1 + - - -
219B GLY* 1.3 70.5 - - - -
221B SER* 1.3 60.5 + - - +
222B GLY 3.9 0.9 - - - -
242B GLY 4.7 1.3 - - - +
243B HIS* 3.3 22.5 + - + -
602B ZN 2.2 32.1 - - - -
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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