Contacts of the strand formed by residues 294 - 298 (chain B) in PDB entry 4R7P
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 THR 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LYS* 5.3 3.4 - - - +
292B GLY 4.8 2.5 - - - +
293B GLY* 1.3 74.8 - - - -
295B LEU* 1.3 72.5 + - - +
296B THR* 3.7 4.0 + - - +
304B LEU* 3.9 5.8 - - - +
305B VAL* 2.9 27.5 + - - +
318B PHE* 3.7 29.2 - - + +
324B PHE* 4.1 27.5 - - + +
326B ILE* 2.5 36.5 + - - +
327B PHE* 4.4 1.3 - - - +
328B ASN 4.9 0.7 - - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO* 4.2 10.2 - - + +
86B ILE* 4.2 14.8 - - + -
280B MET* 3.7 43.7 - - + -
282B VAL* 4.4 11.0 - - + -
294B THR* 1.3 81.7 + - - +
296B THR* 1.3 72.6 + - - +
302B LEU* 4.0 28.3 - - + -
303B ARG 3.2 14.1 - - - +
304B LEU* 3.9 16.2 - - + -
324B PHE* 4.8 4.0 - - - -
326B ILE* 4.0 10.7 - - + +
328B ASN* 6.2 0.2 - - + -
376B ILE* 4.4 6.3 - - + -
384B GLY* 4.2 12.6 - - - -
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 2.7 51.4 - - + +
79B GLN 3.0 13.0 - - - +
80B ARG* 4.4 3.1 - - - -
81B PRO* 4.3 6.3 - - + -
294B THR* 3.7 9.9 + - - +
295B LEU* 1.3 80.3 + - - +
297B GLN* 1.3 69.2 + - - +
298B TYR* 3.6 2.0 + - - -
302B LEU* 3.4 8.9 - - - -
303B ARG* 2.7 44.9 + - - +
305B VAL* 4.0 17.8 - - - +
318B PHE* 5.5 0.5 - - - -
324B PHE* 4.7 0.2 - - - -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS 3.2 14.1 - - - +
78B ILE* 3.9 1.4 + - - +
79B GLN* 3.2 40.0 + - + +
80B ARG 4.0 2.9 - - - +
81B PRO* 3.9 15.9 - - + -
82B PRO* 3.2 32.2 - - + +
85B SER* 4.5 3.9 + - - -
296B THR* 1.3 75.8 - - - +
298B TYR* 1.3 59.1 + - - +
300B GLY* 4.3 12.7 + - - +
301B LYS* 2.9 39.8 - - - +
302B LEU* 3.3 8.3 + - - +
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Residues in contact with TYR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B SER 5.2 2.0 + - - -
73B VAL* 4.7 12.1 - - + -
74B ASP* 3.6 46.5 + - + +
77B LYS* 4.0 16.8 - - - +
78B ILE* 4.1 9.6 - - + -
296B THR* 3.6 2.8 + - - +
297B GLN* 1.3 74.3 - - - +
299B GLU* 1.3 86.4 + - + +
300B GLY 3.0 2.2 - - - -
301B LYS* 2.8 33.3 + - - +
303B ARG* 3.1 62.4 + - + +
305B VAL* 6.1 1.6 - - + -
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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