Contacts of the helix formed by residues 414 - 425 (chain B) in PDB entry 6T2C
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 MET 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B GLU* 3.3 21.8 + - + +
259B ALA* 3.7 21.1 - - + +
260B ARG* 4.1 22.9 - - + +
263B CYS* 3.5 29.3 - - + -
271B LEU* 3.9 35.7 - - + -
272B PRO* 4.1 20.2 - - + -
413B ASN* 1.3 83.2 - - + +
415B LEU* 1.3 59.7 + - - +
416B SER 3.3 1.6 - - - -
417B THR* 3.3 4.3 + - - -
418B VAL* 2.9 30.5 + - - +
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Residues in contact with LEU 415 (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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255B VAL* 4.3 15.7 - - + +
256B GLU* 4.6 3.4 + - - +
258B LEU* 6.0 3.4 - - + -
259B ALA* 3.7 24.7 - - + +
262B ILE* 6.1 0.2 - - + -
318B PHE* 3.6 35.4 - - + +
321B MET* 3.6 28.5 - - + +
322B VAL* 3.8 30.1 - - + -
325B ILE* 4.7 11.4 - - + -
341B PRO* 5.9 0.4 - - + -
412B PHE* 4.7 14.6 - - + -
413B ASN 4.5 1.0 - - - +
414B MET* 1.3 74.5 - - - +
416B SER* 1.3 60.5 + - - +
418B VAL* 3.2 10.5 + - + +
419B LEU* 3.0 24.1 + - - +
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Residues in contact with SER 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 3.5 30.9 - - - -
313B GLN* 2.6 39.2 + - - -
318B PHE* 3.7 7.4 - - - -
412B PHE 3.2 15.0 + - - -
413B ASN* 4.7 4.0 - - - -
414B MET 3.3 0.4 - - - -
415B LEU* 1.3 78.1 - - - +
417B THR* 1.3 57.7 + - - +
419B LEU* 3.3 7.8 + - - +
420B GLY* 3.0 24.9 + - - -
442B GLN* 4.8 0.7 + - - -
444B SER 4.5 2.7 - - - -
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Residues in contact with THR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B CYS* 3.9 10.5 - - - -
269B SER* 3.8 24.0 - - - +
271B LEU* 3.9 8.2 - - + +
413B ASN 3.2 15.8 + - - -
414B MET* 3.3 11.5 + - - -
415B LEU 3.3 0.4 - - - -
416B SER* 1.3 74.9 - - - +
418B VAL* 1.3 59.4 + - - +
420B GLY* 3.4 0.6 + - - +
421B VAL* 2.9 30.6 + - + +
442B GLN* 3.5 32.0 - - - +
443B SER* 4.8 1.6 - - - -
444B SER* 3.4 21.0 + - - -
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 4.4 11.4 - - + -
95B LEU* 4.3 11.3 - - + +
103B PHE* 5.9 1.1 - - + -
259B ALA* 4.6 3.1 - - + +
262B ILE* 4.0 25.4 - - + -
263B CYS* 3.7 16.8 - - - -
266B LEU* 4.6 2.7 - - + -
321B MET* 3.8 16.6 - - + -
325B ILE* 4.6 11.7 - - + -
414B MET 2.9 19.4 + - - +
415B LEU* 3.2 17.9 + - + +
417B THR* 1.3 76.4 - - - +
419B LEU* 1.3 51.6 + - - +
421B VAL* 3.3 7.1 + - - +
422B SER* 2.7 37.4 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 4.3 16.2 - - + -
91B LEU* 5.2 5.4 - - + -
92B ILE* 5.1 3.8 - - + -
309B TRP* 6.1 0.9 - - + -
313B GLN* 5.6 8.3 - - + +
317B ILE* 4.6 9.6 - - + -
318B PHE* 5.3 7.6 - - + -
321B MET* 4.0 24.9 - - + -
415B LEU 3.0 12.9 + - - +
416B SER* 3.3 9.8 + - - +
418B VAL* 1.3 79.1 - - - +
420B GLY* 1.3 62.2 + - - +
422B SER* 3.2 14.2 + - - +
423B VAL* 3.1 25.2 + - - +
473B VAL* 4.2 37.5 - - + +
475B ILE* 4.3 14.6 - - + -
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Residues in contact with GLY 420 (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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416B SER 3.0 12.0 + - - -
417B THR 3.8 1.8 - - - -
418B VAL 3.4 0.2 - - - -
419B LEU* 1.3 76.9 - - - +
421B VAL* 1.3 57.7 + - - +
423B VAL* 3.2 5.3 + - - +
424B LEU* 2.9 32.0 + - - +
442B GLN* 3.7 28.3 - - - +
475B ILE* 4.0 14.5 - - - +
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Residues in contact with VAL 421 (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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95B LEU* 4.5 5.4 - - + -
266B LEU* 3.7 40.8 - - + -
268B GLN* 3.3 43.9 + - + +
269B SER* 4.3 9.6 - - - -
417B THR* 2.9 27.3 + - + +
418B VAL 3.8 3.8 - - - +
420B GLY* 1.3 72.8 - - - +
422B SER* 1.3 59.2 + - - +
424B LEU* 3.3 6.9 + - + +
425B ASN* 2.8 28.6 + - - +
442B GLN* 4.6 6.1 - - + -
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Residues in contact with SER 422 (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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91B LEU* 3.9 38.1 - - - +
92B ILE* 3.6 14.4 - - - +
95B LEU* 3.4 20.7 - - - +
418B VAL 2.7 21.2 + - - -
419B LEU* 3.2 11.4 + - - -
421B VAL* 1.3 77.6 - - - +
423B VAL* 1.3 61.6 + - - +
425B ASN* 3.2 7.9 + - - +
426B LEU* 3.0 20.6 + - - +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.9 21.3 - - + -
419B LEU* 3.1 14.8 + - + +
420B GLY* 3.2 6.9 + - - +
422B SER* 1.3 76.5 - - - +
424B LEU* 1.3 61.9 + - - +
426B LEU* 3.2 20.1 + - - +
438B TRP* 3.5 10.4 + - + -
466B PHE* 3.8 15.9 - - + -
469B THR* 4.3 20.6 - - + -
470B CYS* 3.8 25.6 - - - +
473B VAL* 4.4 10.5 - - + -
475B ILE* 4.3 16.6 - - + -
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Residues in contact with LEU 424 (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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268B GLN* 3.9 21.6 + - + +
420B GLY 2.9 16.0 + - - +
421B VAL* 3.3 7.8 + - - +
423B VAL* 1.3 77.1 - - - +
425B ASN* 1.3 59.5 + - - +
426B LEU 3.6 0.3 + - - -
427B GLY* 3.7 2.9 + - - -
428B GLN* 5.8 0.3 - - - +
438B TRP* 3.6 20.9 + - + +
439B ASP* 4.1 12.3 - - - +
440B GLY 3.8 13.7 - - - +
441B LEU 3.7 30.1 - - - +
442B GLN* 3.8 18.8 - - + +
447B PHE* 5.3 3.1 - - + -
448B ALA 5.1 2.0 - - - +
449B LEU* 3.7 31.9 - - + -
466B PHE* 4.0 17.0 - - + -
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Residues in contact with ASN 425 (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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94B GLY 4.5 6.3 + - - -
95B LEU* 4.0 18.8 - - + +
98B SER* 3.0 29.0 + - - -
99B HIS* 3.7 17.0 - - - -
268B GLN* 3.6 21.2 + - - +
421B VAL 2.8 17.8 + - - +
422B SER 3.2 5.6 + - - +
424B LEU* 1.3 73.6 - - - +
426B LEU* 1.3 64.1 + - - +
427B GLY 3.2 2.2 + - - -
428B GLN* 3.5 27.8 + - - +
431B ILE* 5.1 3.1 - - - +
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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