Contacts of the strand formed by residues 247 - 257 (chain K) 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 PHE 247 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D SER* 5.3 9.2 - - - -
240K GLU* 5.4 9.4 - - + +
241K VAL 4.0 2.7 - - - +
242K SER* 3.8 26.0 - - - -
243K THR 4.6 8.3 - - - -
246K LYS* 1.3 88.6 - - - +
248K ASP* 1.3 66.4 + - - +
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Residues in contact with ASP 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K GLY* 3.8 10.6 - - - -
156K LEU* 3.4 39.3 + - + +
157K PHE* 3.9 24.8 + - + +
240K GLU* 3.5 7.1 - - - +
241K VAL 3.0 33.9 + - - +
247K PHE* 1.3 78.4 - - - +
249K CYS* 1.3 79.9 + - - +
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Residues in contact with CYS 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K PHE* 4.0 5.5 - - - -
160K ARG* 4.7 7.8 + - - -
238K ARG* 4.0 32.8 - - + +
239K CYS 3.1 13.0 - - - +
240K GLU* 4.2 13.7 - - + -
248K ASP* 1.3 89.6 + - - +
250K SER* 1.3 63.5 + - - +
251K ASN* 5.6 2.5 - - - -
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Residues in contact with SER 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K PHE* 3.4 24.0 - - - -
160K ARG* 3.6 27.1 + - - +
161K PRO* 3.6 24.6 + - - +
238K ARG* 3.5 0.9 - - - +
239K CYS* 2.8 31.9 + - - +
249K CYS* 1.3 77.0 - - - +
251K ASN* 1.3 75.3 + - - +
252K PHE* 4.3 1.4 + - - -
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Residues in contact with ASN 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K ARG* 5.1 5.6 + - - +
161K PRO 5.3 1.2 - - - +
163K ASP* 4.7 0.9 - - - +
236K SER* 5.3 7.4 - - - +
237K TYR 3.8 3.8 - - - +
238K ARG* 3.2 37.3 + - - +
249K CYS* 5.6 2.4 - - - -
250K SER* 1.3 89.0 + - - +
252K PHE* 1.3 63.6 + - - +
253K ASN* 5.9 0.7 - - - -
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Residues in contact with PHE 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K PRO* 3.5 34.1 - - + +
162K GLN 4.4 6.1 - - - -
163K ASP* 3.3 12.8 - - - +
174K PHE* 3.6 33.0 - + - -
191K TRP* 3.5 39.5 - + - -
224K LEU* 4.3 3.1 - - + -
236K SER* 4.1 0.7 + - - -
237K TYR* 2.7 78.2 + + + +
239K CYS* 4.0 12.1 - - + -
250K SER 4.6 0.4 - - - -
251K ASN* 1.3 76.5 - - - +
253K ASN* 1.3 72.8 + - - +
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Residues in contact with ASN 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K ASP* 2.8 27.2 + - - +
164K GLY 3.6 22.7 + - - +
174K PHE* 4.7 0.5 - - - -
235K GLY 3.5 7.1 - - - +
236K SER* 3.3 26.2 + - - -
251K ASN 5.7 0.4 - - - -
252K PHE* 1.3 86.3 - - - +
254K LEU* 1.3 61.7 + - - +
255K THR* 5.1 5.5 + - - +
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Residues in contact with LEU 254 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164K GLY 3.5 15.5 - - - +
166K VAL* 4.1 10.3 - - + -
172K ILE* 3.9 17.7 - - + -
174K PHE* 3.7 21.5 - - + -
226K ILE* 3.4 32.5 - - + -
233K PHE* 3.7 23.6 - - + +
234K THR* 3.3 5.9 - - - +
235K GLY 3.0 32.1 + - - +
237K TYR* 3.6 27.5 - - + +
252K PHE* 5.0 0.4 - - - -
253K ASN* 1.3 73.4 - - - +
255K THR* 1.3 65.6 + - - +
256K VAL* 4.6 7.4 - - + -
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Residues in contact with THR 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K GLY 3.4 7.5 + - - -
165K GLU* 3.5 20.3 + - + +
166K VAL* 3.0 26.2 + - - +
234K THR* 4.1 11.7 - - + +
253K ASN* 4.2 6.1 + - - +
254K LEU* 1.3 78.0 + - - +
256K VAL* 1.3 67.8 + - - +
257K HIS* 3.4 33.3 + - + +
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Residues in contact with VAL 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K VAL* 3.4 27.1 - - + +
167K THR 4.7 2.0 - - - -
168K VAL* 4.2 11.7 - - + -
229K ALA* 4.4 6.1 - - + -
230K GLN* 3.4 37.9 - - - +
231K PRO* 4.0 8.6 - - + +
233K PHE* 4.4 8.7 - - + -
234K THR* 3.1 29.3 + - - +
254K LEU* 4.6 4.3 - - + -
255K THR* 1.3 80.3 - - - +
257K HIS* 1.3 75.0 + - - +
258K GLU* 5.4 0.2 - - - +
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Residues in contact with HIS 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K GLU* 3.7 31.2 + - + -
166K VAL 3.4 10.4 + - - +
167K THR* 4.3 7.2 - - + -
168K VAL* 3.1 23.2 + - - +
255K THR* 3.4 33.6 - - + +
256K VAL* 1.3 76.5 + - - +
258K GLU* 1.3 75.6 + - + +
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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