Contacts of the strand formed by residues 211 - 215 (chain L) in PDB entry 4WEB
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 211 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118L ALA* 4.2 18.8 - - + -
119L PRO* 3.1 31.4 - - + +
121L VAL* 3.6 31.2 - - + +
200L CYS 4.1 0.5 - - - +
201L GLU* 3.6 0.2 - - - -
202L ALA* 2.8 40.4 + - + +
207L SER* 6.1 2.5 - - - -
209L SER 3.6 5.0 + - - +
210L PRO* 1.3 71.9 - - - +
212L VAL* 1.3 65.6 + - - +
213L LYS* 4.4 7.6 + - - -
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Residues in contact with VAL 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L THR* 4.7 7.9 - - + -
200L CYS 3.8 2.5 - - - +
201L GLU* 3.5 35.2 - - + +
210L PRO* 3.8 19.1 - - + +
211L ILE* 1.3 81.2 - - - +
213L LYS* 1.3 73.6 + - - +
214L SER* 5.7 0.4 - - - -
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Residues in contact with LYS 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L VAL* 3.2 53.8 - - + +
122L SER* 4.4 2.0 - - - +
123L ILE* 3.4 28.6 - - + +
199L THR* 3.3 2.7 - - - +
200L CYS* 3.1 32.9 + - - -
211L ILE* 4.3 6.7 - - - -
212L VAL* 1.3 83.7 - - - +
214L SER* 1.3 61.4 + - - +
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Residues in contact with SER 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H VAL* 5.0 4.9 - - - +
123L ILE* 3.9 8.4 - - - +
197L SER* 4.7 3.5 + - - -
198L TYR 2.5 14.8 + - - -
199L THR* 2.2 35.4 + - - -
212L VAL* 5.7 0.4 - - - -
213L LYS* 1.3 76.2 - - - +
215L PHE* 1.3 69.3 + - - +
216L ASN* 6.3 0.2 - - - -
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Residues in contact with PHE 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H VAL* 4.1 24.5 - - + -
123L ILE* 3.8 20.4 - - + -
125L PRO* 3.6 27.6 - - + -
138L VAL* 3.5 28.7 - - + -
192L TYR* 3.6 23.6 - + - -
197L SER* 3.0 23.6 - - - -
198L TYR* 3.1 47.8 + + + -
214L SER* 1.3 80.5 + - - +
216L ASN* 1.3 82.8 + - - +
217L ARG 4.7 4.0 - - - -
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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