Contacts of the helix formed by residues 434 - 443 (chain C) in PDB entry 4Z2C
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 434 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C VAL* 3.1 13.8 + - - +
433C GLU* 1.3 74.9 - - - +
435C ASP* 1.3 61.5 + - - -
436C SER* 3.2 7.1 + - - -
438C GLY* 2.9 18.4 + - - -
454C PRO* 4.2 6.1 - - - +
455C ILE 3.2 14.4 + - - -
456C ARG* 4.8 6.5 - - - +
457C GLY 5.4 1.7 - - - +
2F A 3.3 10.8 - - - -
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Residues in contact with ASP 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 3.6 5.9 + - - -
114A SER 5.3 1.2 - - - +
116A ALA* 5.5 0.2 - - - -
415C LYS* 5.7 2.1 - - - +
434C GLY* 1.3 71.0 - - - -
436C SER* 1.3 58.0 + - - +
438C GLY* 3.2 10.0 - - - +
439C GLY* 2.9 21.4 + - - +
454C PRO* 3.9 24.6 - - - +
2F A 2.7 45.3 + - - +
3F T 5.6 2.0 + - - -
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Residues in contact with SER 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 3.1 30.1 + - - +
116A ALA* 3.8 20.1 - - - +
117A ALA* 3.5 19.2 + - - +
120A TYR* 3.6 27.3 - - - -
433C GLU 5.3 2.5 - - - -
434C GLY* 3.2 1.5 - - - -
435C ASP* 1.3 78.4 - - - +
437C ALA* 1.3 57.5 + - - +
440C SER* 3.9 1.0 + - - -
588C GLY* 3.5 11.6 - - - -
1F G 4.6 2.8 + - - -
2F A 3.8 13.9 + - - -
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Residues in contact with ALA 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C VAL* 3.6 19.7 - - + -
433C GLU 3.9 10.0 + - - +
434C GLY 3.5 1.8 + - - -
436C SER* 1.3 77.1 - - - +
438C GLY* 1.3 59.6 + - - +
439C GLY 3.3 0.7 - - - -
440C SER* 3.3 5.3 + - - -
441C ALA* 2.9 31.7 + - - +
506C ASP* 4.8 2.9 - - - +
587C LEU* 3.6 35.7 - - + -
588C GLY* 4.1 8.3 - - - +
595C LEU* 4.6 2.5 - - + +
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Residues in contact with GLY 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C VAL* 3.5 8.5 - - - +
434C GLY 2.9 17.4 + - - -
435C ASP* 3.2 11.3 + - - -
437C ALA* 1.3 78.5 - - - +
439C GLY* 1.3 55.6 + - - +
441C ALA* 3.9 2.8 - - - +
442C LYS* 2.9 32.9 + - - +
452C ILE* 4.3 4.3 - - - +
454C PRO* 4.6 12.6 - - - -
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Residues in contact with GLY 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 3.5 20.0 - - - -
109A SER* 5.7 0.2 - - - -
113A ASP* 4.9 15.7 - - - -
114A SER 5.4 0.4 - - - -
435C ASP* 2.9 12.4 + - - +
437C ALA 3.3 0.4 - - - -
438C GLY* 1.3 72.8 - - - +
440C SER* 1.3 60.6 - - - +
442C LYS* 3.4 4.1 + - - +
443C SER* 2.9 35.2 + - - -
592C ASP* 4.8 0.4 - - - +
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Residues in contact with SER 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 3.3 24.0 - - - +
436C SER 3.9 2.9 + - - -
437C ALA 3.3 7.9 + - - -
439C GLY* 1.3 76.2 - - - +
441C ALA* 1.3 63.0 + - - +
443C SER 3.6 14.6 - - - +
444C GLY* 4.1 4.2 + - - +
587C LEU 4.0 8.2 + - - -
590C MET 3.3 23.7 + - - -
591C ASP 4.6 3.8 - - - -
592C ASP* 4.1 15.7 + - - +
595C LEU* 3.6 24.2 - - - +
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C VAL* 4.3 10.3 - - + -
437C ALA 2.9 17.5 + - - +
438C GLY 3.9 0.2 - - - +
440C SER* 1.3 79.0 - - - +
442C LYS* 1.3 63.9 + - - +
443C SER 3.3 0.7 + - - -
444C GLY 3.7 3.3 + - - +
445C ARG* 3.1 24.4 - - - +
452C ILE* 3.6 35.7 - - + -
504C MET* 5.4 1.8 - - - -
595C LEU* 3.5 14.3 - - + +
600C MET* 4.5 7.4 - - + -
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Residues in contact with LYS 442 (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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111A ASP* 5.7 0.5 - - - +
417C ALA* 4.3 18.2 - - + -
438C GLY 2.9 20.8 + - - +
439C GLY* 3.9 4.7 - - - +
441C ALA* 1.3 75.1 - - - +
443C SER* 1.3 61.6 + - - +
444C GLY 3.4 3.6 + - - -
445C ARG* 2.4 40.5 + - - +
452C ILE* 4.0 5.5 - - + +
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Residues in contact with SER 443 (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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109A SER* 3.2 34.1 + - - -
111A ASP* 4.2 9.9 + - - -
113A ASP* 5.2 1.6 - - - +
295A ARG* 5.1 3.1 - - - +
439C GLY 2.9 17.2 + - - -
440C SER 3.6 3.9 - - - +
442C LYS* 1.3 79.0 - - - +
444C GLY* 1.3 54.5 + - - +
592C ASP* 3.2 34.2 - - - +
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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