Contacts of the strand formed by residues 235 - 242 (chain H) in PDB entry 6G2T
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 GLY 235 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193H LYS* 5.8 3.1 - - - -
233H PHE 3.5 2.9 + - - -
234H THR* 1.3 78.8 - - - +
236H SER* 1.3 60.6 + - - -
237H TYR* 4.8 5.6 - - - -
253H ASN* 3.6 6.3 - - - +
254H LEU* 3.0 34.2 + - - +
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Residues in contact with SER 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193H LYS* 4.4 1.6 - - - +
194H GLY* 3.0 28.3 + - - -
235H GLY* 1.3 72.5 - - - -
237H TYR* 1.3 70.0 + - - +
251H ASN* 5.3 7.3 - - - +
252H PHE 4.0 2.4 + - - -
253H ASN* 3.3 20.5 + - - -
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Residues in contact with TYR 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H PHE* 5.0 0.2 - + - -
191H TRP* 5.9 0.2 - - + -
192H PHE 3.3 5.4 - - - +
193H LYS* 3.5 38.8 - - + +
199H LEU* 4.9 13.0 - - + +
202H LYS* 5.8 0.3 + - - -
207H LEU* 5.9 3.5 - - + +
224H LEU* 4.6 7.6 - - + -
226H ILE* 4.0 12.7 - - + +
233H PHE* 2.9 44.1 + - - +
235H GLY 4.1 4.9 + - - -
236H SER* 1.3 87.8 + - - +
238H ARG* 1.3 60.7 + - - +
251H ASN* 3.8 2.3 - - - +
252H PHE* 2.8 73.7 + + + +
254H LEU* 3.5 29.6 - - + +
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Residues in contact with ARG 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H LYS 4.0 0.7 - - - +
191H TRP* 3.7 1.9 - - - -
192H PHE* 2.7 64.9 + - + +
194H GLY 4.5 10.1 - - - +
195H LYS* 3.9 33.4 - - - +
236H SER 4.4 0.2 + - - -
237H TYR* 1.3 75.2 - - - +
239H CYS* 1.3 62.4 + - - +
240H GLU* 4.0 5.1 + - + +
249H CYS* 3.7 35.0 - - + +
250H SER 3.5 5.2 - - - +
251H ASN* 3.2 30.6 + - - +
252H PHE* 4.5 2.0 - - - -
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Residues in contact with CYS 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PHE* 3.9 20.2 - - + -
161H PRO* 3.8 19.3 - - + -
176H ALA* 4.2 5.2 - - - -
189H VAL* 3.9 15.9 - - - -
190H LYS 3.8 2.7 - - - -
191H TRP* 3.6 44.6 - - + -
238H ARG* 1.3 71.9 - - - +
240H GLU* 1.3 61.6 + - - +
241H VAL* 4.3 0.2 - - - -
249H CYS* 3.2 5.3 - - - -
250H SER* 2.9 37.8 + - - +
252H PHE* 4.0 2.6 - - + -
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Residues in contact with GLU 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H VAL 3.9 0.7 - - - +
189H VAL* 3.3 2.6 - - - +
190H LYS* 2.7 61.3 + - + +
192H PHE* 3.4 28.3 - - + -
238H ARG* 4.0 4.9 + - + +
239H CYS* 1.3 72.3 - - - +
241H VAL* 1.3 68.3 + - - +
242H SER* 4.4 5.8 - - - +
247H PHE* 5.6 8.5 - - + +
248H ASP 3.6 12.8 - - - +
249H CYS* 4.3 9.8 - - + +
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Residues in contact with VAL 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H LEU* 3.5 10.5 - - + +
157H PHE* 3.2 32.9 - - + -
176H ALA* 5.2 0.4 - - + -
178H VAL* 3.7 22.7 - - + -
187H PRO* 3.8 19.1 - - + -
188H VAL 3.3 8.1 - - - +
189H VAL* 3.5 24.5 - - + -
222H PHE* 4.1 10.8 - - + -
239H CYS* 4.3 2.2 + - - -
240H GLU* 1.3 79.6 - - - +
242H SER* 1.3 63.7 + - - +
243H THR* 4.8 2.0 - - + -
247H PHE* 4.2 0.2 - - - -
248H ASP* 3.1 30.2 + - - +
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Residues in contact with SER 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H PRO* 3.3 6.6 - - - +
188H VAL* 2.8 51.9 + - - +
190H LYS* 6.2 0.3 - - - -
240H GLU* 4.4 6.2 - - - +
241H VAL* 1.3 75.4 - - - +
243H THR* 1.3 62.9 + - - +
246H LYS 3.8 3.1 - - - -
247H PHE* 3.7 26.5 - - - -
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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