Contacts of the helix formed by residues 427 - 438 (chain C) in PDB entry 6AH0
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 427 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315C SER 5.8 2.0 - - - -
317C CYS* 4.8 15.0 - - - +
424C PHE 4.7 1.4 + - - -
425C GLY 3.6 2.6 + - - -
426C GLU* 1.3 75.4 - - - +
428C THR* 1.3 64.5 + - - +
429C GLY 3.7 2.6 + - - -
430C PHE* 4.1 7.5 + - - -
431C VAL* 4.1 5.9 + - - -
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Residues in contact with THR 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PRO 5.6 5.6 - - - -
192C ASP* 5.7 4.6 - - - +
193C THR 5.7 4.5 + - - +
317C CYS 4.4 3.8 + - - -
322C SER* 6.3 0.4 - - - -
424C PHE 5.3 2.8 + - - -
426C GLU* 4.8 1.4 - - - +
427C PHE* 1.3 74.8 - - - +
429C GLY* 1.3 66.3 + - - +
430C PHE 3.3 2.2 - - - -
431C VAL* 3.2 3.4 + - - +
432C ASP* 2.9 20.6 + - - -
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Residues in contact with GLY 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C CYS* 6.0 5.2 - - - -
317C CYS 4.0 15.4 + - - -
318C PHE* 4.8 2.7 - - - +
319C THR* 4.6 17.0 - - - -
322C SER* 5.7 7.6 - - - +
427C PHE 3.7 0.8 - - - -
428C THR* 1.3 73.7 - - - +
430C PHE* 1.3 62.8 + - - +
432C ASP* 3.2 2.5 + - - -
433C MET* 2.9 20.6 + - - -
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Residues in contact with PHE 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C CYS* 6.5 0.7 - - - +
317C CYS* 5.6 2.2 - - - +
427C PHE 4.1 5.1 + - - -
428C THR 3.3 0.8 - - - -
429C GLY* 1.3 74.8 - - - +
431C VAL* 1.3 58.3 + - - +
433C MET* 3.2 3.0 + - - +
434C CYS* 2.9 26.0 + - - -
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Residues in contact with VAL 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ASP* 5.9 6.5 - - - +
427C PHE 4.1 5.9 + - - -
428C THR* 3.2 8.5 + - - +
430C PHE* 1.3 75.1 - - - +
432C ASP* 1.3 62.4 + - - +
434C CYS* 3.2 2.2 + - - +
435C VAL* 2.9 21.3 + - - -
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Residues in contact with ASP 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ASP* 5.8 3.4 - - - +
193C THR 6.2 0.9 - - - +
428C THR 2.9 14.0 + - - -
429C GLY* 3.7 3.4 - - - -
431C VAL* 1.3 76.4 - - - +
433C MET* 1.3 62.9 + - - +
435C VAL* 3.2 1.3 + - - +
436C GLN* 2.9 22.7 + - - -
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Residues in contact with MET 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C GLY 4.4 17.3 - - - -
306C ASN* 5.8 2.2 - - - +
429C GLY 2.9 14.0 + - - -
430C PHE* 3.7 3.8 - - - +
432C ASP* 1.3 75.7 - - - +
434C CYS* 1.3 62.6 + - - +
436C GLN* 5.2 0.4 - - - +
437C HIS* 3.0 24.9 + - - -
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Residues in contact with CYS 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ARG* 6.0 1.9 - - - -
430C PHE 2.9 14.7 + - - -
431C VAL* 3.2 4.0 + - - +
433C MET* 1.3 77.7 - - - +
435C VAL* 1.3 62.4 + - - +
437C HIS 5.7 0.2 - - - -
438C ILE* 3.3 20.9 + - - +
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Residues in contact with VAL 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C VAL 2.9 14.6 + - - -
432C ASP* 3.8 1.8 - - - +
434C CYS* 1.3 76.5 - - - +
436C GLN* 1.3 61.2 + - - +
437C HIS 3.8 0.2 + - - -
438C ILE 4.1 9.5 - - - +
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Residues in contact with GLN 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C ASP 2.9 16.0 + - - -
433C MET* 3.7 0.4 - - - +
435C VAL* 1.3 79.2 - - - +
437C HIS* 1.3 57.4 + - - +
438C ILE 5.0 1.1 - - - +
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Residues in contact with HIS 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C ALA* 5.3 9.9 - - - -
433C MET 3.0 15.1 + - - -
436C GLN* 1.3 72.5 - - - +
438C ILE* 1.3 60.0 + - - +
439C PRO 3.9 1.4 - - - -
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Residues in contact with ILE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLY* 6.1 4.5 - - - -
434C CYS* 3.3 18.9 + - - +
435C VAL 4.1 9.5 - - - +
436C GLN 3.5 1.5 - - - +
437C HIS* 1.3 78.5 - - - +
439C PRO* 1.3 63.3 - - - +
440C SER* 3.2 4.8 + - - +
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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