Contacts of the strand formed by residues 302 - 308 (chain B) in PDB entry 4TR8
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 GLU 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG 4.0 0.3 - - - +
106A PHE* 3.4 2.4 - - - -
107A THR* 2.7 49.8 + - + +
274B LEU* 3.4 5.4 - - - +
283B ARG* 5.3 0.9 + - - -
294B GLN* 2.7 29.6 + - + +
295B ALA 3.4 11.0 - - - +
296B ASN* 4.5 4.5 - - + +
300B GLN 3.8 4.7 + - - +
301B GLU* 1.3 75.2 - - - +
303B ALA* 1.3 70.1 + - - +
304B GLU* 4.7 12.4 - - + +
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Residues in contact with ALA 303 (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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105A ARG 3.4 4.9 - - - -
106A PHE* 3.7 23.1 - - + -
271B THR* 3.5 35.7 - - - +
274B LEU* 4.0 8.0 - - + +
293B ILE 4.5 0.4 - - - -
294B GLN* 3.3 5.6 - - - +
295B ALA 2.9 30.6 + - - +
302B GLU* 1.3 75.1 - - - +
304B GLU* 1.3 65.5 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG 3.8 1.1 - - - +
104A SER* 3.5 1.7 - - - -
105A ARG* 2.7 51.8 + - + +
106A PHE* 5.5 1.1 - - - -
271B THR* 4.4 1.6 - - - -
283B ARG* 4.7 6.8 + - - -
285B GLN* 5.2 2.1 + - - -
292B LYS* 4.7 18.5 - - - +
293B ILE 3.2 4.5 - - - +
294B GLN* 3.7 23.7 - - + +
302B GLU* 4.7 13.7 - - + +
303B ALA* 1.3 80.0 - - - +
305B GLU* 1.3 60.4 - - - +
306B GLU* 6.1 2.2 - - + +
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Residues in contact with GLU 305 (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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103A ARG* 3.5 8.3 - - + +
104A SER* 3.2 21.8 + - - +
106A PHE* 5.2 1.0 - - + -
263B GLN* 4.9 5.5 + - - +
267B ALA* 3.4 29.0 - - + +
270B ARG* 2.7 48.5 + - - +
271B THR* 3.8 15.1 - - + +
291B LEU 3.7 1.6 - - - +
292B LYS* 3.5 2.6 - - - +
293B ILE* 2.8 36.7 + - + +
304B GLU* 1.3 74.2 - - - +
306B GLU* 1.3 70.8 + - - +
307B VAL* 4.1 6.5 - - - +
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Residues in contact with GLU 306 (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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103A ARG* 3.2 41.8 + - + +
263B GLN* 4.9 3.6 + - - -
290B LEU* 3.9 19.4 - - + +
291B LEU 3.6 3.8 - - - -
292B LYS* 3.5 38.2 + - + +
304B GLU* 6.0 2.2 - - + +
305B GLU* 1.3 79.5 - - - +
307B VAL* 1.3 63.3 + - - +
308B GLN 4.4 0.3 + - - -
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Residues in contact with VAL 307 (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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260B ASP 5.7 1.3 - - - +
263B GLN* 3.5 37.2 - - + +
264B LEU* 4.0 24.9 - - + -
267B ALA* 3.8 17.7 - - + -
290B LEU* 3.7 5.1 - - - +
291B LEU* 2.8 40.4 + - + +
293B ILE* 3.8 24.7 - - + -
305B GLU* 4.2 5.2 - - - +
306B GLU* 1.3 77.3 - - - +
308B GLN* 1.3 72.1 + - - +
309B VAL* 3.4 4.7 + - + +
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Residues in contact with GLN 308 (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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259B GLY* 5.1 3.5 - - - -
260B ASP 5.3 1.0 + - - -
263B GLN* 4.2 12.0 - - - +
289B GLY 3.6 10.7 + - - +
290B LEU* 4.8 5.6 - - + +
306B GLU 4.3 0.8 + - - -
307B VAL* 1.3 81.2 - - - +
309B VAL* 1.3 62.9 + - - +
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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