Contacts of the strand formed by residues 370 - 374 (chain B) in PDB entry 1TTT
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 PHE 370 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B PHE 3.8 0.3 - - - +
317B GLU* 3.3 7.8 - - - +
318B ALA* 3.0 30.9 + - + +
320B VAL* 3.8 35.2 - - + -
322B ILE* 4.9 1.3 - - + -
334B PHE* 4.4 16.6 - + - -
342B PHE* 5.1 0.4 - + - -
353B VAL* 3.4 30.1 - - + -
354B ARG 3.5 15.3 - - - +
355B LEU* 3.8 15.0 - - + -
356B PRO* 4.7 3.4 - - - -
368B VAL* 3.5 40.4 - - + -
369B THR* 1.3 75.9 - - - +
371B THR* 1.3 63.4 + - - +
372B VAL* 4.1 20.0 - - + -
388B ILE* 4.7 11.9 - - + -
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Residues in contact with THR 371 (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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315B LYS* 4.4 11.9 - - - +
316B PHE 3.1 8.7 + - - +
317B GLU* 4.4 8.1 + - - +
352B VAL 3.5 2.3 - - - +
353B VAL* 3.8 0.7 - - - -
354B ARG* 3.2 43.5 + - + +
370B PHE* 1.3 81.4 + - - +
372B VAL* 1.3 84.9 + - - +
373B GLU* 4.2 12.1 - - - +
404B LEU* 3.7 12.9 - - + +
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR 4.1 0.4 - - - -
315B LYS* 3.0 4.0 - - - -
316B PHE* 2.6 58.7 + - + +
318B ALA* 5.2 2.2 - - + -
342B PHE* 3.3 52.3 - - + -
351B GLY* 3.8 4.7 - - - -
352B VAL 3.4 17.7 - - - +
353B VAL* 5.2 0.7 - - + -
370B PHE* 4.1 17.0 - - + -
371B THR* 1.3 85.2 - - - +
373B GLU* 1.3 64.4 - - - +
374B LEU* 4.1 6.5 - - + -
386B PHE* 5.7 0.2 - - + -
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Residues in contact with GLU 373 (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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314B THR* 3.2 6.7 - - - -
315B LYS* 3.6 39.9 + - + -
351B GLY* 3.5 0.3 - - - -
352B VAL* 3.0 32.9 + - + +
354B ARG* 2.3 49.2 + - - +
371B THR* 4.4 1.9 - - - +
372B VAL* 1.3 73.8 - - - +
374B LEU* 1.3 64.8 + - - +
375B ILE* 3.9 1.2 + - - +
24D G 5.2 3.6 + - - +
25D C 5.0 4.9 - - - +
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Residues in contact with LEU 374 (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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313B HIS 4.3 0.9 - - - +
314B THR* 2.5 39.7 + - - +
316B PHE* 3.7 24.9 - - + -
342B PHE* 4.2 16.8 - - + -
344B PHE* 4.3 4.5 - - + -
349B VAL* 4.0 20.2 - - + +
350B THR 3.7 4.5 - - - +
351B GLY* 4.0 16.8 - - - -
372B VAL* 4.3 4.7 - - + -
373B GLU* 1.3 75.9 - - - +
375B ILE* 1.3 61.3 + - - +
376B LYS 3.0 22.1 + - - +
378B VAL* 4.2 26.7 - - + -
380B LEU* 4.2 6.7 - - + -
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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