Contacts of the strand formed by residues 291 - 299 (chain A) in PDB entry 3R6O
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.7 4.2 - - - +
203A PRO* 3.9 2.5 - - - -
204A TRP* 3.3 27.6 - - - -
286A HIS* 3.5 3.5 + - - -
287A SER 3.0 33.0 + - - +
288A ALA 4.5 0.8 + - - -
289A LYS 3.6 0.2 - - - -
290A LEU* 1.3 80.7 - - - +
292A LYS* 1.3 61.4 + - - -
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 4.3 3.8 - - - +
122A ARG* 5.8 1.2 - - - +
165A LEU* 4.6 0.4 - - - -
203A PRO* 3.3 23.5 - - - +
285A ALA 3.1 11.4 - - - +
286A HIS* 4.7 9.9 - - + +
291A GLY* 1.3 74.4 - - - +
293A MET* 1.3 66.8 + - - +
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.2 16.4 - - + +
165A LEU* 3.5 32.8 - - + +
166A ALA* 3.8 8.1 - - - +
167A ASN* 5.0 2.9 - - - -
200A PRO* 3.6 9.9 - - + +
201A THR* 3.5 26.7 - - - +
202A GLY 3.3 27.4 - - - +
283A ILE 4.0 0.9 - - - +
284A GLU* 3.4 7.1 - - - +
285A ALA* 2.8 43.4 + - + +
292A LYS* 1.3 78.1 - - - +
294A ARG* 1.3 61.5 + - - +
295A LEU* 4.2 25.8 - - + -
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO 3.0 7.3 + - - -
122A ARG* 3.2 33.6 - - + +
282A VAL* 3.6 40.8 - - + +
283A ILE 3.2 4.0 - - - +
284A GLU* 4.8 8.3 + - + -
293A MET* 1.3 74.4 - - - +
295A LEU* 1.3 60.7 + - - +
296A PRO* 3.5 20.4 - - - +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY 3.7 7.9 - - - +
121A PRO 3.4 32.8 - - - +
123A ASP 3.4 20.0 - - - +
125A VAL* 4.1 14.4 - - + -
167A ASN* 5.0 6.3 - - + +
200A PRO* 3.6 32.5 - - + -
282A VAL* 3.5 3.3 - - - -
283A ILE* 2.8 62.7 + - + +
293A MET* 4.2 17.5 - - + -
294A ARG* 1.3 73.7 - - - +
296A PRO* 1.3 66.8 - - - +
297A VAL* 3.7 1.6 + - - +
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Residues in contact with PRO 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG 3.8 13.0 - - - +
124A ALA* 3.1 26.5 - - + +
125A VAL 3.0 23.2 + - - -
281A ASP 3.7 6.7 - - - +
282A VAL* 4.4 11.8 - - + -
294A ARG* 3.5 24.5 - - - +
295A LEU* 1.3 83.7 - - - +
297A VAL* 1.3 59.5 + - - +
298A HIS* 4.0 15.9 - - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 3.4 12.6 - - + +
127A ALA* 5.0 1.3 - - + -
134A LEU* 4.9 9.0 - - + -
277A LEU* 4.1 23.6 - - + -
278A ARG 3.5 23.8 - - - +
280A GLY* 2.9 26.9 + - - -
281A ASP* 2.9 29.5 + - + +
283A ILE* 4.0 26.2 - - + -
295A LEU 4.2 1.3 - - - +
296A PRO* 1.3 75.8 - - - +
298A HIS* 1.3 72.7 + - - +
299A ASP* 4.5 8.7 - - - +
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Residues in contact with HIS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ALA* 3.9 23.3 - - + +
125A VAL 3.1 5.5 + - - -
126A ILE* 3.2 21.2 - - + +
127A ALA 3.0 21.8 + - - -
279A PRO* 4.9 2.9 - - - -
280A GLY* 5.9 1.8 + - - -
296A PRO* 4.0 18.6 - - - +
297A VAL* 1.3 81.3 + - - +
299A ASP* 1.3 68.0 + - - +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 5.1 0.4 - - - -
127A ALA* 3.4 23.9 - - - +
131A SER 6.0 1.3 - - - -
277A LEU 5.2 2.3 - - - +
278A ARG 4.7 0.3 - - - -
279A PRO* 3.5 43.9 - - + +
297A VAL* 4.5 3.1 - - - +
298A HIS* 1.3 78.5 - - - +
300A GLU* 1.3 69.6 + - - +
301A LYS* 3.5 6.4 + - - +
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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