Contacts of the helix formed by residues 425 - 434 (chain C) in PDB entry 3CMM
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 GLY 425 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C PRO 5.1 0.4 - - - -
409C THR* 3.5 26.5 - - - -
410C THR* 3.9 1.6 - - - +
421C ILE* 2.9 21.5 + - - -
423C VAL 3.7 0.4 - - - -
424C PHE* 1.3 80.8 - - - +
426C LEU* 1.3 64.6 + - - -
427C ASP 3.5 2.2 - - - -
428C PHE 3.6 1.1 + - - -
429C GLN* 3.3 21.5 + - - +
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Residues in contact with LEU 426 (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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409C THR* 3.1 16.6 + - - +
411C GLN 6.0 0.2 - - - +
413C VAL* 4.6 19.5 - - + -
421C ILE* 4.1 28.6 - - + +
425C GLY* 1.3 71.2 - - - -
427C ASP* 1.3 64.4 + - - +
429C GLN* 3.1 8.3 + - + +
430C LYS* 3.0 53.9 + - + +
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Residues in contact with ASP 427 (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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402C ASN 5.6 2.1 - - - +
403C PHE* 3.9 21.6 - - + -
404C PRO* 6.1 0.9 - - - +
409C THR* 5.7 0.9 + - - -
425C GLY 3.5 0.4 - - - -
426C LEU* 1.3 83.6 - - - +
428C PHE* 1.3 57.9 + - - +
430C LYS* 3.4 9.7 + - - +
431C LYS* 3.1 26.0 + - - +
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Residues in contact with PHE 428 (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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398C PRO* 4.0 20.2 - - + -
403C PHE* 3.6 37.1 - + + -
424C PHE* 3.7 54.3 - + + +
425C GLY 3.6 2.0 + - - +
426C LEU 3.3 0.8 - - - -
427C ASP* 1.3 76.9 - - - +
429C GLN* 1.3 64.1 - - - +
431C LYS* 3.1 4.1 + - + +
432C ILE* 3.1 31.3 + - + +
882C TYR* 3.5 39.7 - + + -
885C ILE* 3.6 30.7 - - + -
886C ASP* 4.0 9.4 - - - -
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Residues in contact with GLN 429 (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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417C TYR* 4.2 15.9 - - + -
420C GLN* 3.1 48.8 + - - +
421C ILE* 3.8 21.8 - - + -
424C PHE* 4.2 14.1 - - - +
425C GLY 3.3 10.1 + - - +
426C LEU* 3.3 11.9 - - + +
428C PHE* 1.3 79.0 - - - +
430C LYS* 1.3 57.4 + - + +
432C ILE* 3.4 22.9 + - - +
433C ALA* 3.1 22.0 + - - +
456C LEU 3.4 17.3 - - - +
882C TYR* 5.6 0.6 - - - -
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Residues in contact with LYS 430 (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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426C LEU* 3.0 42.4 + - + +
427C ASP* 3.9 10.1 - - - +
428C PHE 3.2 0.2 - - - -
429C GLN* 1.3 75.0 - - + +
431C LYS* 1.3 62.7 + - - +
432C ILE 3.3 0.2 - - - -
433C ALA* 3.3 11.3 + - + +
434C ASN* 2.8 37.1 + - - +
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Residues in contact with LYS 431 (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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403C PHE* 3.7 28.3 - - + -
427C ASP 3.1 14.2 + - - +
428C PHE* 3.1 11.6 + - + +
430C LYS* 1.3 75.3 - - - +
432C ILE* 1.3 65.9 + - - +
434C ASN* 3.2 13.8 + - + +
435C SER* 3.1 18.6 + - - -
885C ILE* 3.4 40.3 + - + +
887C ASN* 4.5 15.8 + - - +
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Residues in contact with ILE 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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428C PHE* 3.1 29.1 + - + +
429C GLN* 3.4 28.7 - - - +
431C LYS* 1.3 76.5 - - - +
433C ALA* 1.3 64.5 - - - +
434C ASN 3.0 1.7 + - - -
435C SER* 3.0 22.7 + - - -
456C LEU* 3.8 23.1 - - + +
458C LEU* 3.6 32.6 - - + -
459C GLY 3.5 6.8 + - - -
881C LEU* 5.3 1.6 - - + -
882C TYR* 3.8 29.4 - - + -
885C ILE* 4.3 21.5 - - + -
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Residues in contact with ALA 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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429C GLN 3.1 10.9 + - - +
430C LYS* 3.4 19.7 - - + +
431C LYS 3.2 0.2 - - - -
432C ILE* 1.3 80.1 - - - +
434C ASN* 1.3 55.2 + - - +
435C SER 3.4 0.2 - - - -
457C GLY 3.4 13.2 - - - +
459C GLY* 3.2 6.6 + - - -
460C SER* 3.2 24.6 + - - +
461C GLY* 2.5 32.8 + - - +
464C GLY* 3.9 0.5 - - - -
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Residues in contact with ASN 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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430C LYS* 2.8 29.3 + - - +
431C LYS* 3.2 10.8 + - + +
432C ILE 3.0 1.8 + - - -
433C ALA* 1.3 76.0 - - - +
435C SER* 1.3 59.7 + - - +
436C LYS* 4.4 2.6 - - - +
461C GLY* 3.4 3.2 - - - -
462C SER* 3.4 11.8 + - - -
463C ASP* 2.9 55.5 + - + +
464C GLY* 3.5 7.0 - - - -
537C ASP* 3.9 4.7 - - - +
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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