Contacts of the strand formed by residues 303 - 311 (chain F) in PDB entry 6CP3
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 SER 303 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132F GLU* 5.2 6.5 + - - -
149F ARG* 5.7 3.4 - - - -
150F GLY* 4.5 11.1 - - - -
244F ARG* 4.6 0.3 - - - +
249F GLN 3.3 6.4 + - - +
250F ASP* 3.4 23.8 + - - -
251F VAL* 2.9 26.7 + - - +
298F THR* 3.8 15.0 - - - +
302F GLY* 1.3 74.9 - - - -
304F VAL* 1.3 66.1 + - - +
305F THR* 4.0 5.4 - - - -
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Residues in contact with VAL 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F GLY* 3.4 11.5 - - - +
151F GLY 3.3 13.0 - - - +
152F LYS* 5.3 0.5 - - - +
240F ALA* 4.9 6.3 - - + +
241F GLU* 5.5 0.7 - - - -
244F ARG* 3.7 28.3 - - + +
251F VAL* 3.3 19.1 - - + +
253F LEU* 4.2 19.5 - - + -
295F ARG 5.9 0.2 - - - +
296F ILE* 3.8 29.3 - - + +
297F THR* 3.3 22.2 + - - +
298F THR* 3.6 7.4 + - - -
303F SER* 1.3 78.3 - - - +
305F THR* 1.3 61.9 + - - +
306F SER* 3.7 2.2 + - - -
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Residues in contact with THR 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F LEU* 4.8 5.6 - - + -
148F ALA 3.4 24.0 - - - +
149F ARG* 3.3 25.5 + - - -
150F GLY* 2.4 22.5 + - - -
151F GLY 3.7 3.8 - - - +
153F ILE* 4.2 16.4 - - + -
178F HIS* 5.7 1.3 - - - -
251F VAL 2.9 9.7 + - - -
252F LEU* 3.3 32.8 - - + +
253F LEU 3.6 6.8 + - - -
303F SER* 4.0 4.6 - - - -
304F VAL* 1.3 70.6 - - - +
306F SER* 1.3 57.7 + - - +
307F VAL* 4.1 3.0 + - + +
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Residues in contact with SER 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F GLY 3.7 5.5 + - - -
152F LYS* 3.3 24.9 - - - +
153F ILE* 3.0 26.5 + - - +
253F LEU* 3.1 27.4 - - - +
296F ILE* 3.5 23.0 - - - +
304F VAL* 3.7 1.5 - - - -
305F THR* 1.3 74.0 - - - +
307F VAL* 1.3 61.4 + - - +
308F GLN* 3.7 13.1 + - - +
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Residues in contact with VAL 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ILE* 3.5 34.1 - - + +
155F LEU* 4.2 24.5 - - + -
167F ILE* 4.5 10.0 - - + +
170F LEU* 4.4 18.6 - - + -
174F ILE* 5.8 4.3 - - + -
252F LEU* 6.0 1.8 - - + -
253F LEU 2.9 5.9 + - - -
254F PHE* 3.4 32.0 - - + -
255F ILE 2.9 25.1 + - - +
305F THR* 4.9 4.9 - - + +
306F SER* 1.3 76.6 - - - +
308F GLN* 1.3 60.7 + - - +
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Residues in contact with GLN 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LYS* 4.2 2.0 - - - +
153F ILE 2.8 15.0 + - - +
154F GLY* 3.5 3.9 - - - -
155F LEU* 3.1 21.8 + - - +
255F ILE* 3.4 23.9 - - + +
258F ILE* 4.3 13.8 - - + +
293F GLN* 2.7 38.1 + - - +
296F ILE* 3.4 31.3 - - - +
306F SER* 3.7 18.1 + - - +
307F VAL* 1.3 79.2 - - - +
309F ALA* 1.3 69.4 + - - +
310F VAL* 4.3 3.1 - - + +
325F THR* 5.2 1.2 - - - +
329F LEU* 4.2 13.5 - - + +
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Residues in contact with ALA 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F LEU* 3.8 13.2 - - + +
163F LYS* 4.4 13.5 - - + -
167F ILE* 3.7 19.9 - - + +
255F ILE 2.9 9.6 + - - +
256F ASP* 3.6 18.2 - - - +
257F ASN* 3.0 23.6 + - - +
258F ILE* 3.2 15.9 + - - +
307F VAL 4.2 0.6 + - - -
308F GLN* 1.3 76.0 - - - +
310F VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F LEU 3.0 11.4 + - - +
156F PHE* 3.6 35.1 - - + -
157F GLY 3.0 26.0 + - - +
163F LYS* 3.7 3.1 - - - +
257F ASN* 3.5 2.2 - - - +
258F ILE* 3.7 18.8 - - + -
259F PHE* 4.7 4.5 - - + -
308F GLN* 4.3 7.4 - - + +
309F ALA* 1.3 78.8 - - - +
311F TYR* 1.3 71.9 + - - +
312F VAL* 4.2 0.4 - - + +
321F ALA 5.8 0.2 - - - -
322F PRO* 3.8 16.2 - - + -
325F THR* 3.8 20.0 - - + +
329F LEU* 4.8 4.7 - - + -
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Residues in contact with TYR 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B THR* 2.4 33.4 + - - -
343B ASN* 4.5 6.5 - - - -
346B SER* 3.7 13.8 + - - -
157F GLY 3.7 3.6 - - - -
159F ALA* 3.4 33.7 - - + +
163F LYS* 3.9 19.3 - - - -
257F ASN* 3.2 26.5 - - - +
259F PHE* 3.2 41.2 - + + +
260F ARG* 3.3 33.9 - - - +
310F VAL* 1.3 80.6 - - - +
312F VAL* 1.3 79.0 + - - +
313F PRO* 4.1 7.8 - - + +
322F PRO* 4.9 1.0 - - - +
600F ADP 4.9 0.2 - - - -
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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