Contacts of the helix formed by residues 321 - 330 (chain G) in PDB entry 6IY6
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 321 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197G ARG* 3.2 23.8 - - + -
198G LEU* 3.8 29.2 - - + -
201G GLY* 3.5 25.8 - - - -
204G HIS* 6.3 2.2 - + - -
205G LEU* 4.7 6.7 - - + -
316G GLY 4.2 1.1 - - - -
317G LEU* 3.0 35.6 + - + +
320G ARG* 1.3 99.4 - - + +
322G GLN* 1.3 56.7 + - - +
323G THR 3.3 2.7 - - - -
324G GLU* 3.4 22.2 + - + +
325G ILE* 3.1 29.6 + - - +
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Residues in contact with GLN 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G LEU 3.6 1.2 + - - -
318G GLN* 2.7 41.9 + - - +
319G GLU 4.3 7.6 - - - +
320G ARG 3.2 4.4 + - - +
321G PHE* 1.3 73.8 - - - +
323G THR* 1.3 65.6 + - + +
325G ILE* 3.4 20.2 + - - +
326G GLN* 3.2 44.1 + - + +
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Residues in contact with THR 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ARG* 5.8 4.4 + - - +
84G GLN* 4.8 4.5 - - - -
85G PHE* 5.3 14.6 - - + -
320G ARG 4.6 5.1 + - - +
321G PHE 4.5 0.2 - - - -
322G GLN* 1.3 79.3 + - + +
324G GLU* 1.3 80.9 + - - -
326G GLN* 3.6 4.9 + - - +
327G THR* 2.6 36.2 + - - -
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Residues in contact with GLU 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLN* 2.8 26.1 + - - +
85G PHE* 5.0 4.0 - - - -
194G ALA* 3.2 48.6 - - - +
197G ARG* 4.3 18.5 - - + -
198G LEU* 4.3 10.5 - - + -
320G ARG 4.6 0.9 - - - +
321G PHE* 3.4 31.8 + - + +
322G GLN 3.3 0.6 - - - -
323G THR* 1.3 94.6 + - - +
325G ILE* 1.3 65.0 + - - +
327G THR* 3.5 1.3 + - - -
328G VAL* 3.4 14.1 + - - +
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Residues in contact with ILE 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G LEU* 3.6 16.8 - - + -
317G LEU 3.4 25.4 - - - +
318G GLN* 4.2 10.8 - - + -
321G PHE 3.1 19.5 + - - +
322G GLN* 3.7 22.0 - - - +
323G THR 3.4 0.2 - - - -
324G GLU* 1.3 75.9 - - - +
326G GLN* 1.3 54.3 + - + +
328G VAL* 3.3 6.4 + - - +
329G ASN* 2.9 33.0 + - + +
336G PRO* 6.3 3.1 - - + -
480G PHE* 4.0 20.2 - - + -
481G LEU* 4.4 15.0 - - + +
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Residues in contact with GLN 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322G GLN* 3.2 35.0 + - + +
323G THR* 4.0 5.6 - - - +
325G ILE* 1.3 74.6 - - - +
327G THR* 1.3 56.6 + - - +
329G ASN* 3.3 25.1 + - - +
330G LYS* 2.8 45.8 + - + +
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Residues in contact with THR 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLN* 4.1 14.6 + - + +
190G SER* 3.1 46.0 + - - +
191G THR* 4.1 10.2 + - - -
194G ALA* 3.7 6.3 - - + -
323G THR 2.6 24.5 + - - -
324G GLU* 3.6 7.4 - - - -
325G ILE 3.3 0.2 - - - -
326G GLN* 1.3 78.3 - - - +
328G VAL* 1.3 58.7 - - - +
330G LYS* 3.8 23.7 - - + +
331G GLN* 4.1 2.3 + - - +
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Residues in contact with VAL 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G THR* 3.9 10.5 - - + +
194G ALA* 3.8 12.8 - - + -
195G VAL* 3.6 30.3 - - + +
198G LEU* 6.3 0.2 - - + -
324G GLU 3.4 14.6 - - - +
325G ILE 3.3 7.3 + - - +
326G GLN 3.3 0.2 - - - -
327G THR* 1.3 73.9 - - - +
329G ASN* 1.3 54.7 + - - +
330G LYS 3.3 0.4 - - - -
331G GLN* 3.3 4.3 + - - +
332G PHE* 2.8 40.6 + - + +
481G LEU* 4.1 24.0 - - + +
483G LEU* 3.9 28.9 - - + -
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Residues in contact with ASN 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G ILE* 2.9 18.8 + - + +
326G GLN* 3.3 32.8 + - - +
328G VAL* 1.3 75.9 - - - +
330G LYS* 1.3 62.4 + - - +
332G PHE 3.2 20.4 - - - -
333G PRO* 3.2 10.2 - - - +
334G CYS* 3.1 34.2 + - + +
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Residues in contact with LYS 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G SER 6.0 0.2 + - - -
131G THR* 5.7 7.5 - - - +
326G GLN* 2.8 29.0 + - + +
327G THR* 3.8 19.3 + - + +
328G VAL 3.3 0.4 - - - -
329G ASN* 1.3 74.6 - - - +
331G GLN* 1.3 57.2 + - - +
333G PRO* 5.2 3.5 - - - +
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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