Contacts of the helix formed by residues 532 - 541 (chain C) in PDB entry 4C1M
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 SER 532 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C ILE* 4.4 5.6 - - - -
294C ARG* 3.7 12.8 - - - +
295C ASP* 5.3 0.2 - - - -
530C GLN 3.7 4.2 + - - -
531C ILE* 1.3 79.8 - - - +
533C LEU* 1.3 62.9 + - - +
534C PRO* 3.2 12.1 - - - +
535C ARG* 3.4 19.4 + - - +
536C ILE* 3.2 22.4 + - - +
549C ASN* 3.7 25.6 + - - -
567C LEU* 4.9 4.0 - - - +
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Residues in contact with LEU 533 (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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85A MET* 4.0 22.2 - - + -
89A TRP* 3.9 31.4 - - + -
249C MET* 4.1 15.9 - - + -
252C LEU* 4.1 16.6 - - + -
253C LEU* 6.2 2.0 - - + -
291C ILE* 4.0 23.3 - - + +
295C ASP* 5.1 2.2 + - - -
532C SER* 1.3 68.8 - - - +
534C PRO* 1.4 73.9 - - + +
536C ILE* 3.1 9.6 + - + +
537C ILE* 3.0 29.6 + - + +
551C ILE* 3.8 28.2 - - + +
552C PHE* 4.2 10.5 - - + -
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Residues in contact with PRO 534 (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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532C SER* 3.2 12.1 - - - +
533C LEU* 1.4 93.2 - - + +
535C ARG* 1.3 56.4 + - - +
537C ILE* 3.4 13.7 + - + +
538C CYS* 2.9 34.7 + - - -
546C VAL* 3.6 18.6 - - + +
547C SER 3.3 27.4 - - - +
549C ASN* 3.7 17.9 - - - +
551C ILE* 4.0 21.1 - - + -
567C LEU* 3.9 8.1 - - + -
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Residues in contact with ARG 535 (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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530C GLN 5.8 1.8 - - - +
531C ILE* 6.3 0.2 - - - -
532C SER* 3.4 23.0 + - - +
533C LEU 3.2 0.4 - - - -
534C PRO* 1.3 77.3 - - - +
536C ILE* 1.3 59.4 + - + +
538C CYS* 3.2 14.4 + - - +
539C ASP* 2.9 69.1 + - - +
564C CYS* 3.0 23.8 + - - +
565C SER* 4.8 2.4 - - - +
567C LEU* 2.8 40.4 + - + +
568C PRO 3.5 22.9 - - - +
569C ALA* 3.6 23.3 - - - +
570C LEU 5.0 1.6 - - - +
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Residues in contact with ILE 536 (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 LEU* 4.0 21.9 - - + +
253C LEU* 5.1 11.0 - - + -
256C GLU* 4.2 18.4 - - + +
287C MET* 3.6 38.4 - - + -
291C ILE* 3.9 27.6 - - + -
531C ILE* 4.7 3.6 - - + -
532C SER 3.2 11.9 + - - +
533C LEU* 3.1 13.2 + - + +
535C ARG* 1.3 75.9 - - + +
537C ILE* 1.3 60.8 + - - +
539C ASP* 3.4 2.7 + - - -
540C ASN* 2.8 44.1 + - - +
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Residues in contact with ILE 537 (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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85A MET* 4.2 12.3 - - + -
252C LEU* 3.8 26.7 - - + -
381C LEU* 4.9 6.7 - - + -
385C MET* 4.0 16.8 - - + -
533C LEU* 3.0 26.7 + - + +
534C PRO* 3.4 6.1 - - + +
536C ILE* 1.3 72.6 - - - +
538C CYS* 1.3 62.7 + - - +
539C ASP 3.2 0.2 + - - -
540C ASN 3.2 0.9 + - - -
541C THR* 2.6 43.8 + - + +
543C ILE* 4.1 17.0 - - + -
546C VAL* 3.9 18.2 - - + -
551C ILE* 3.7 26.9 - - + -
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Residues in contact with CYS 538 (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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534C PRO 2.9 25.5 + - - -
535C ARG* 3.2 20.8 + - - +
537C ILE* 1.3 75.4 - - - +
539C ASP* 1.3 61.6 + - - +
540C ASN 3.5 0.2 + - - -
541C THR 3.7 12.0 - - - +
543C ILE 4.0 6.9 - - - +
546C VAL* 3.6 13.2 - - - -
564C CYS* 2.0 60.7 - - + -
567C LEU* 4.3 4.5 - - - -
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Residues in contact with ASP 539 (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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208C ARG* 5.7 0.9 + - - -
256C GLU* 4.5 1.9 - - - +
259C ARG* 3.7 45.2 + - - +
535C ARG* 2.9 56.8 + - - +
536C ILE* 3.9 4.6 - - - +
537C ILE 3.2 0.6 - - - -
538C CYS* 1.3 76.3 - - - +
540C ASN* 1.3 66.6 + - - +
541C THR 3.7 0.9 - - - -
569C ALA* 4.6 6.6 - - - +
570C LEU 5.3 1.4 + - - -
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Residues in contact with ASN 540 (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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208C ARG* 3.4 8.7 - - - -
252C LEU* 3.8 13.5 + - + +
255C ARG* 2.8 54.7 + - + +
256C GLU* 2.8 51.2 + - - +
259C ARG* 3.5 15.8 - - - +
536C ILE* 2.8 27.4 + - - +
537C ILE 3.2 1.8 + - - -
539C ASP* 1.3 84.7 - - - +
541C THR* 1.3 57.1 + - - +
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Residues in contact with THR 541 (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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208C ARG* 3.5 20.0 + - - +
252C LEU* 3.7 10.1 - - + -
255C ARG* 4.2 0.4 - - - +
377C ILE* 4.1 6.5 - - + -
378C ASP* 3.4 16.8 - - - +
381C LEU* 3.5 31.9 - - + -
537C ILE 2.6 22.0 + - - +
538C CYS 3.7 11.6 - - - +
539C ASP 4.9 0.7 - - - -
540C ASN* 1.3 84.4 + - - +
542C GLY* 1.3 62.0 + - - +
543C ILE* 3.2 25.9 + - + +
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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