Contacts of the strand formed by residues 336 - 341 (chain A) 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 GLN 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A VAL* 3.8 18.9 - - + +
259A GLY* 3.3 15.0 + - - +
260A ASP* 4.9 3.6 - - - +
261A ARG 4.5 0.4 - - - -
310A GLU* 3.1 26.5 + - - +
332A ILE* 4.0 0.5 - - - +
334A THR* 2.7 31.9 + - - +
335A GLU* 1.3 92.5 - - + +
337A VAL* 1.3 62.1 - - - +
353A ALA* 3.5 23.8 + - + +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL 3.5 1.4 - - - +
258A VAL* 3.4 6.4 - - - +
259A GLY 2.9 33.8 + - - +
261A ARG* 4.1 8.1 - - + -
264A LEU* 3.6 30.5 - - + -
329A LEU* 3.8 22.7 - - + -
332A ILE* 3.9 16.6 - - + -
336A GLN* 1.3 74.9 - - - +
338A ARG* 1.3 66.5 + - - +
339A PHE* 3.8 10.2 - - + -
350A VAL* 3.5 28.7 - - + -
351A HIS 3.6 8.3 - - - +
353A ALA 4.8 0.4 - - - +
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Residues in contact with ARG 338 (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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256A LEU* 4.0 25.3 - - + +
257A VAL 3.3 3.6 - - - -
258A VAL* 4.1 15.5 - - + -
337A VAL* 1.3 76.2 - - - +
339A PHE* 1.3 62.1 + - - +
340A ILE* 4.1 10.9 - - + +
349A LEU 3.7 0.7 - - - +
350A VAL* 3.2 8.7 - - - +
351A HIS* 3.0 54.7 + - + +
352A GLU 3.0 18.1 + - - +
353A ALA* 3.5 19.0 + - - +
354A ASP 4.7 0.8 - - - -
355A ASN* 2.9 27.7 + - - +
356A ASP* 2.7 31.3 + - - -
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Residues in contact with PHE 339 (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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255A LYS 3.6 1.6 - - - +
256A LEU* 3.5 4.2 - - - +
257A VAL* 2.8 56.9 + - + +
264A LEU* 4.1 13.7 - - + -
268A PHE* 4.5 17.7 - + - -
284A LEU* 5.7 6.7 - - + -
320A PHE* 5.9 2.9 - + - -
325A LEU* 4.0 23.6 - - + -
328A VAL* 6.0 1.3 - - + -
329A LEU* 4.3 15.7 - - + -
337A VAL* 3.8 30.1 - - + -
338A ARG* 1.3 76.8 - - - +
340A ILE* 1.3 62.3 + - - +
341A LEU* 4.5 11.7 - - + -
348A ALA* 4.6 11.7 - - + -
349A LEU 3.4 4.3 - - - -
350A VAL* 3.7 26.0 - - + -
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Residues in contact with ILE 340 (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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250A PRO* 5.6 0.3 - - - +
253A GLY* 3.7 33.8 - - - +
255A LYS 3.4 6.5 - - - +
256A LEU* 3.9 18.8 - - + -
338A ARG* 4.7 11.9 - - + +
339A PHE* 1.3 76.3 - - - +
341A LEU* 1.3 62.1 + - - +
347A SER 4.3 1.7 - - - +
348A ALA* 3.8 1.4 - - - -
349A LEU* 2.7 54.0 + - + +
351A HIS* 3.7 33.4 - - + +
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Residues in contact with LEU 341 (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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253A GLY* 3.5 3.5 - - - -
254A ASP 3.2 6.8 + - - -
255A LYS* 2.8 40.5 + - + +
257A VAL* 4.0 13.2 - - + -
284A LEU* 6.0 2.7 - - + -
286A LEU* 3.5 31.2 - - + -
316A LEU* 4.1 19.3 - - + -
318A ILE* 4.6 14.4 - - + -
320A PHE* 4.5 10.5 - - + -
339A PHE* 4.5 16.4 - - + -
340A ILE* 1.3 73.7 - - - +
342A SER* 1.3 63.2 + - - +
346A SER 5.8 0.2 - - - +
347A SER 4.9 4.3 - - - +
348A ALA* 3.5 34.8 - - + -
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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