Contacts of the helix formed by residues 430 - 440 (chain B) in PDB entry 6CNC
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 430 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B THR* 6.3 0.7 - - + -
150B GLY* 3.2 9.5 - - - -
151B ARG* 2.4 62.3 + - + +
427B ASN* 3.2 15.2 + - + -
429B ILE* 1.3 76.0 - - - +
431B SER* 1.3 60.2 + - - +
432B GLY 3.2 0.4 - - - -
433B LEU* 2.7 24.4 + - - +
434B ASN* 2.7 33.2 + - - +
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Residues in contact with SER 431 (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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427B ASN* 2.7 29.0 + - - +
430B THR* 1.3 75.9 - - - +
432B GLY* 1.3 61.5 + - - -
434B ASN* 3.7 9.8 - - - +
435B ARG* 2.9 30.4 + - - +
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Residues in contact with GLY 432 (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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391B LEU* 3.4 12.7 - - - +
427B ASN 3.2 9.9 + - - -
428B ASN* 3.5 15.5 + - - +
430B THR 3.2 0.2 - - - -
431B SER* 1.3 77.3 - - - +
433B LEU* 1.3 58.9 + - - +
435B ARG* 4.3 7.0 + - - +
436B ALA* 3.3 21.3 + - - +
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Residues in contact with LEU 433 (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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151B ARG 5.0 1.3 - - - +
152B MET* 3.6 21.3 - - + -
153B PRO* 3.5 33.2 - - + -
384B ILE* 5.2 8.7 - - + -
387B LEU* 3.5 34.5 - - + -
388B PHE* 4.9 17.3 - - + +
391B LEU* 3.4 9.6 - - + +
429B ILE* 3.1 20.9 - - + +
430B THR 2.7 11.3 + - - +
432B GLY* 1.3 71.4 - - - +
434B ASN* 1.3 64.7 + - - +
436B ALA* 3.3 3.3 + - - +
437B ILE* 2.9 26.2 + - + +
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Residues in contact with ASN 434 (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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124B THR* 3.2 34.6 + - - +
151B ARG 4.7 2.6 + - - -
153B PRO* 4.4 10.0 - - - +
187B VAL* 3.7 12.4 - - + +
188B ASN* 5.7 8.5 - - - +
430B THR* 2.7 51.9 + - - +
431B SER* 3.7 8.9 - - - +
433B LEU* 1.3 72.0 - - - +
435B ARG* 1.3 64.6 + - - +
437B ILE* 3.0 11.1 + - - +
438B SER* 2.9 26.8 + - - -
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Residues in contact with ARG 435 (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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188B ASN* 6.0 1.3 - - - +
431B SER* 2.9 22.9 + - - +
432B GLY* 4.3 5.6 + - - +
434B ASN* 1.3 71.4 - - - +
436B ALA* 1.3 64.1 + - - +
438B SER* 3.0 7.5 + - - -
439B THR* 2.9 39.4 + - - +
441B ASN 6.0 0.2 + - - -
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Residues in contact with ALA 436 (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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387B LEU* 3.7 30.1 - - + -
432B GLY 3.3 14.6 + - - +
433B LEU 3.3 8.9 + - - +
434B ASN 3.1 0.4 - - - -
435B ARG* 1.3 81.1 - - - +
437B ILE* 1.3 58.3 + - - +
439B THR* 5.2 0.2 - - - -
440B GLY* 2.7 36.3 + - - +
441B ASN 4.1 11.3 + - - +
442B TRP* 4.1 10.5 + - + -
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Residues in contact with ILE 437 (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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153B PRO* 4.9 9.9 - - + -
185B PHE* 4.6 18.8 - - + -
187B VAL* 3.8 29.1 - - + +
191B GLU 6.1 0.4 - - - +
192B LYS* 4.2 5.9 - - + +
193B VAL 5.0 1.6 - - - +
194B ILE* 3.5 37.7 - - + -
384B ILE* 5.5 2.7 - - + -
387B LEU* 5.9 1.6 - - + -
433B LEU* 2.9 21.2 + - + +
434B ASN* 3.0 11.8 + - - +
436B ALA* 1.3 73.4 - - - +
438B SER* 1.3 62.8 + - - +
442B TRP* 4.3 15.7 - - + +
455B THR* 3.3 31.3 + - + +
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Residues in contact with SER 438 (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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187B VAL* 3.7 19.7 - - - -
188B ASN* 4.4 16.3 + - - -
190B THR* 5.7 1.1 - - - -
192B LYS* 2.2 45.1 + - - +
434B ASN 2.9 14.6 + - - -
435B ARG* 3.0 15.1 + - - -
437B ILE* 1.3 77.6 - - - +
439B THR* 1.3 76.7 + - - +
455B THR* 3.8 1.9 + - - -
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Residues in contact with THR 439 (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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192B LYS* 4.5 0.7 - - - +
435B ARG* 2.9 25.4 + - - +
436B ALA* 4.2 1.1 - - - -
438B SER* 1.3 86.2 + - - +
440B GLY* 1.3 59.9 + - - +
441B ASN* 3.2 31.8 + - + +
453B GLY* 5.7 1.6 - - - -
455B THR* 4.1 3.9 + - - +
29Y T 5.9 2.9 - - - +
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Residues in contact with GLY 440 (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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436B ALA 2.7 20.1 + - - -
438B SER 3.5 1.0 - - - -
439B THR* 1.3 73.9 - - - +
441B ASN* 1.3 61.9 + - - +
442B TRP* 3.8 2.9 + - - -
451B ARG 4.9 0.2 - - - -
452B ALA* 3.7 1.6 - - - -
453B GLY* 3.1 24.3 + - - -
454B VAL* 3.5 30.3 + - - +
455B THR* 3.8 10.8 - - - -
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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