Contacts of the helix formed by residues 344 - 356 (chain F) in PDB entry 6VVT
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 344 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338F ALA* 3.7 0.2 - - - -
343F ILE* 1.3 76.7 - - - +
345F PRO* 1.3 72.3 - - - +
346F GLU* 3.0 24.3 - - - +
347F LYS* 2.9 36.2 + - + +
348F VAL* 3.1 11.4 - - - +
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Residues in contact with PRO 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334F PRO* 3.9 21.2 - - + +
335F GLU* 4.4 21.5 - - + +
338F ALA* 3.4 14.1 - - + -
343F ILE 4.0 0.9 - - - +
344F THR* 1.3 86.2 - - - +
346F GLU* 1.3 59.4 + - + +
348F VAL* 3.0 25.3 - - + +
349F LEU* 3.1 20.6 + - + +
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Residues in contact with GLU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F THR* 3.0 29.7 + - - +
345F PRO* 1.3 79.3 - - + +
347F LYS* 1.3 56.1 + - - +
349F LEU* 3.4 13.0 + - + +
350F GLU* 2.9 29.6 + - - +
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Residues in contact with LYS 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F MET* 4.8 18.7 - - - +
343F ILE* 4.4 12.3 - - + -
344F THR* 2.9 32.4 + - + +
346F GLU* 1.3 74.5 - - - +
348F VAL* 1.3 54.3 + - - +
350F GLU* 3.0 31.7 + - - +
351F ILE* 2.6 54.5 + - + +
20O T 3.9 18.5 + - - -
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Residues in contact with VAL 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F LEU* 3.8 23.1 - - + -
334F PRO* 4.2 10.3 - - + +
337F LEU* 4.3 8.5 - - + -
338F ALA* 3.7 17.3 - - + -
343F ILE* 4.3 6.0 - - + +
344F THR 3.1 13.2 - - - +
345F PRO* 3.0 23.3 - - + +
347F LYS* 1.3 73.1 - - - +
349F LEU* 1.3 59.8 + - + +
351F ILE* 3.5 10.1 - - - +
352F GLN* 2.6 62.3 + - - +
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Residues in contact with LEU 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846C ARG* 3.3 33.4 - - - +
854C ALA* 4.2 16.3 - - + +
855C GLY* 4.8 5.8 - - - +
334F PRO* 3.9 29.4 - - + -
345F PRO* 3.1 21.8 + - + +
346F GLU* 3.5 14.8 - - + +
347F LYS 3.1 0.2 - - - -
348F VAL* 1.3 76.0 - - + +
350F GLU* 1.3 65.3 + - - +
352F GLN* 3.0 23.8 + - - +
353F GLN* 3.0 30.6 + - - +
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Residues in contact with GLU 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 4.9 7.3 + - - -
346F GLU 2.9 17.3 + - - +
347F LYS* 3.0 34.4 + - + +
349F LEU* 1.3 72.0 - - - +
351F ILE* 1.3 62.3 + - - +
353F GLN* 3.4 15.9 + - - +
354F TYR* 2.3 62.6 + - + +
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Residues in contact with ILE 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F MET* 4.4 19.1 - - + -
313F VAL* 3.7 26.5 - - + -
314F ILE* 4.0 32.5 - - + +
317F LEU* 4.6 16.6 - - + -
343F ILE* 4.1 15.9 - - + -
347F LYS* 2.6 42.7 + - + +
348F VAL* 3.5 6.5 - - - +
350F GLU* 1.3 71.2 - - - +
352F GLN* 1.3 66.7 + - - +
354F TYR* 3.0 20.8 + - + +
355F ALA* 3.2 11.3 + - + +
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Residues in contact with GLN 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854C ALA* 3.8 18.7 - - + +
317F LEU* 4.3 13.7 - - + +
321F GLN* 3.8 24.0 - - - +
334F PRO* 5.5 2.7 - - - +
337F LEU* 4.0 8.5 - - - +
348F VAL* 2.6 43.2 + - + +
349F LEU* 3.0 24.4 + - - +
351F ILE* 1.3 73.0 - - - +
353F GLN* 1.3 60.5 - - - +
355F ALA* 3.7 14.2 + - - +
356F ARG* 3.8 15.4 + - - +
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Residues in contact with GLN 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752C ASP* 3.9 31.7 + - - +
753C THR* 5.7 1.4 + - - +
854C ALA* 4.1 17.8 + - + +
855C GLY* 3.9 20.4 + - - -
335D PHE* 6.2 0.2 - - - -
349F LEU* 3.0 22.1 + - - +
350F GLU* 3.6 16.6 - - - +
351F ILE 3.1 0.2 - - - -
352F GLN* 1.3 77.3 - - - +
354F TYR* 1.3 70.9 + - + +
355F ALA 3.4 0.3 + - - -
356F ARG* 3.5 20.2 + - - +
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Residues in contact with TYR 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TYR* 3.8 49.3 - + + +
37D ARG* 4.1 23.2 + - + +
302F ARG* 3.8 0.9 + - - -
306F ILE* 3.8 16.8 - - + +
310F MET* 4.0 29.6 - - + -
314F ILE* 4.5 11.4 - - + -
350F GLU* 2.3 57.2 + - + +
351F ILE* 3.0 11.0 + - + +
353F GLN* 1.3 84.1 - - + +
355F ALA* 1.3 61.9 + - - +
356F ARG 3.2 7.6 + - - +
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Residues in contact with ALA 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F ARG* 2.9 29.1 + - - +
314F ILE* 3.9 28.4 - - + +
351F ILE* 3.2 12.8 + - + +
352F GLN* 4.0 9.9 - - - +
353F GLN 3.2 1.2 - - - -
354F TYR* 1.3 76.3 - - - +
356F ARG* 1.3 63.7 + - - +
357F GLU* 3.3 3.6 + - - +
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Residues in contact with ARG 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751C ARG* 4.5 6.1 - - - +
853C PRO* 6.2 1.6 - - - +
332D GLY 4.0 14.3 + - - -
333D GLY 4.5 2.8 + - - -
334D ARG* 3.8 55.2 - - + +
335D PHE* 5.6 7.6 - - + -
302F ARG* 4.1 2.4 + - - -
304F ILE* 6.1 1.4 - - - +
352F GLN 3.8 14.8 - - - +
353F GLN* 3.8 12.9 - - - +
354F TYR 3.2 9.2 - - - +
355F ALA* 1.3 78.2 - - + +
357F GLU* 1.3 63.9 + - - +
358F PRO* 4.7 0.9 - - - +
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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