Contacts of the strand formed by residues 199 - 205 (chain C) in PDB entry 5U2V
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 PHE 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C ARG 3.7 0.5 - - - +
186C VAL* 3.3 4.3 - - - -
187C ASN* 2.9 44.4 + - + +
188C ARG* 5.2 5.8 - - - -
197C ALA* 3.9 26.2 - - + -
198C LEU* 1.3 74.0 - - - +
200C CYS* 1.3 60.5 + - - +
201C LYS* 3.8 29.4 + - + +
214C TRP* 4.1 2.7 - - - -
241C TRP* 4.0 31.0 - + + -
243C SER* 3.6 28.5 - - - +
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Residues in contact with CYS 200 (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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184C VAL* 3.7 16.2 - - - -
185C ARG 3.6 5.2 - - - -
186C VAL* 4.5 2.7 - - - -
198C LEU 4.0 0.4 + - - -
199C PHE* 1.3 70.9 - - - +
201C LYS* 1.3 62.2 + - - +
212C MET* 3.2 16.2 - - + +
214C TRP* 3.5 25.0 - - + +
241C TRP* 3.0 24.8 - - - +
242C ALA* 3.1 6.2 + - + -
243C SER 4.0 4.8 - - - +
256C CYS* 2.0 48.2 - - - -
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Residues in contact with LYS 201 (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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183C LEU 3.5 1.4 - - - +
184C VAL* 3.1 4.6 - - - +
185C ARG* 2.9 76.7 + - + +
187C ASN* 3.6 22.5 - - - +
199C PHE* 4.2 30.7 - - + +
200C CYS* 1.3 77.2 - - - +
202C ALA* 1.3 61.7 + - - +
212C MET* 4.2 1.8 - - - -
240C ALA 3.6 4.5 - - - +
241C TRP* 4.1 14.8 - - + -
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Residues in contact with ALA 202 (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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182C PRO* 4.0 7.0 - - + -
183C LEU 3.1 5.2 - - - +
184C VAL* 3.8 21.5 - - + -
185C ARG* 5.4 0.2 - - - -
201C LYS* 1.3 76.8 - - - +
203C HIS* 1.3 62.7 + - - +
205C PHE* 3.8 17.7 - - + -
210C ILE* 4.4 3.4 - - + -
212C MET* 4.0 17.8 - - + +
239C GLN* 3.2 5.4 - - - +
240C ALA 2.9 32.0 + - - +
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Residues in contact with HIS 203 (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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182C PRO* 3.6 1.6 - - - +
183C LEU* 2.9 67.7 + - + +
185C ARG* 3.6 19.2 + - - +
202C ALA* 1.3 76.6 - - - +
204C GLY* 1.3 69.4 + - - +
205C PHE* 3.3 4.0 + - - -
233C SER* 5.2 0.9 - - - +
238C TYR 3.4 8.3 - - - -
239C GLN* 3.8 18.2 - - + +
12D ARG 4.9 7.6 - - - +
13D HIS* 5.0 8.8 + - - -
14D PRO* 3.6 37.6 - - + +
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Residues in contact with GLY 204 (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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180C GLU* 3.7 15.1 - - - +
181C PRO 3.7 9.9 - - - +
183C LEU* 5.9 3.1 - - - -
203C HIS* 1.3 84.8 - - - +
205C PHE* 1.3 60.2 + - - +
233C SER* 5.0 1.4 + - - -
237C THR* 3.6 25.2 + - - +
238C TYR 3.1 6.1 + - - -
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Residues in contact with PHE 205 (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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180C GLU 3.0 12.3 - - - +
182C PRO* 3.6 31.6 - - + -
202C ALA* 3.8 18.2 - - + -
203C HIS* 3.9 6.1 - - - -
204C GLY* 1.3 79.6 - - - +
206C TYR* 1.3 60.8 + - - +
207C PRO 3.5 13.5 - - - -
208C PRO 3.5 22.9 - - - -
210C ILE* 3.7 22.0 - - + -
230C ILE* 4.2 1.8 - - + -
237C THR* 3.5 5.5 - - - -
238C TYR* 3.0 64.7 + - + -
239C GLN* 3.6 20.2 - - - -
240C ALA* 3.9 3.4 - - + -
260C HIS* 3.9 11.4 - + - +
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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