Contacts of the helix formed by residues 434 - 442 (chain C) in PDB entry 3SRF
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
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Residue Dist Surf HB Arom Phob DC
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431C THR* 3.0 16.5 + - - -
432C GLU 3.5 1.6 - - - -
433C SER* 1.3 77.1 - - - +
435C ARG* 1.3 63.2 + - - +
436C SER 3.1 2.9 - - - -
437C ALA* 2.9 17.1 + - - -
438C HIS* 2.9 33.5 + - - -
458C THR* 3.6 13.1 - - - +
462C ALA* 6.3 0.4 - - - -
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Residues in contact with ARG 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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408C MET* 4.5 4.4 - - + +
433C SER* 3.1 25.3 + - - +
434C GLY* 1.3 74.1 - - - +
436C SER* 1.3 61.4 + - - +
438C HIS* 3.6 12.2 + - - +
439C GLN* 3.4 27.4 + - - +
519C GLY* 2.8 28.1 + - - -
520C PHE* 4.3 9.1 - - - +
531C PO4 3.0 23.7 + - - +
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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
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408C MET* 3.3 27.1 - - - +
429C VAL* 3.9 10.7 - - - +
431C THR* 4.2 1.3 - - - -
434C GLY 2.9 0.2 + - - -
435C ARG* 1.3 70.4 - - - +
437C ALA* 1.3 64.8 + - - +
439C GLN 3.6 3.6 + - - -
440C VAL* 3.4 11.3 - - - +
520C PHE* 4.1 1.0 - - - +
521C THR* 3.3 39.5 + - - -
531C PO4 2.8 39.3 + - - -
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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
----------------------------------------------------------
429C VAL* 3.9 13.6 - - + +
431C THR* 4.2 9.6 + - + -
434C GLY* 2.9 8.3 + - - +
436C SER* 1.3 76.3 - - - +
438C HIS* 1.3 65.9 - - + +
440C VAL* 3.3 8.1 + - - +
441C ALA* 3.1 22.2 + - - +
449C ILE* 4.5 5.6 - - + +
451C ALA* 3.8 28.5 - - + -
462C ALA* 6.1 0.7 - - + -
468C ILE* 3.8 17.4 - - + +
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Residues in contact with HIS 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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265C LYS* 4.5 12.3 + - - -
320C GLY 5.2 2.5 - - - +
433C SER 4.3 5.2 - - - -
434C GLY* 2.9 38.9 + - - +
435C ARG* 3.8 10.6 + - - +
437C ALA* 1.3 77.7 - - + +
439C GLN* 1.3 61.6 + - - +
441C ALA* 3.5 3.2 + - - +
442C ARG* 3.2 26.7 + - - +
458C THR* 5.6 1.4 + - + +
461C GLN* 4.6 3.0 + - + -
462C ALA* 4.5 11.3 - - + +
465C TYR* 3.2 66.8 + + + -
468C ILE* 3.8 12.3 - - + -
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Residues in contact with GLN 439 (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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406C ASP* 4.6 4.3 + - - -
408C MET* 4.0 16.4 - - + -
409C GLU* 3.3 39.7 + - + +
412C ALA* 3.4 5.5 - - + +
435C ARG* 3.4 16.7 + - - +
436C SER 4.0 2.9 - - - +
437C ALA 3.2 0.8 - - - -
438C HIS* 1.3 82.1 - - - +
440C VAL* 1.3 64.7 + - - +
442C ARG* 2.9 45.0 - - - +
443C TYR* 3.2 25.9 - - + -
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Residues in contact with VAL 440 (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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408C MET* 4.4 2.5 - - + -
412C ALA* 3.9 17.7 - - + +
416C VAL* 3.8 19.5 - - + -
427C LEU* 3.8 19.7 - - + -
429C VAL* 4.3 7.4 - - + -
436C SER 3.4 16.6 - - - +
437C ALA 3.3 7.1 + - - +
439C GLN* 1.3 77.2 - - - +
441C ALA* 1.3 62.9 + - - +
443C TYR* 3.0 16.3 + - - +
445C PRO* 3.3 16.2 - - + +
449C ILE* 3.8 22.2 - - + -
511C LEU* 4.0 23.6 - - + -
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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
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356C ASP* 5.6 1.9 - - - +
437C ALA 3.1 13.2 + - - +
438C HIS 3.7 9.2 - - - +
440C VAL* 1.3 78.4 - - - +
442C ARG* 1.3 58.5 + - - +
444C ARG* 3.1 28.8 + - - -
445C PRO* 4.3 2.4 - - - +
449C ILE* 3.7 14.1 - - + +
465C TYR* 4.2 12.8 - - + -
466C ARG* 3.3 25.2 - - - +
468C ILE* 4.1 10.8 - - + -
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Residues in contact with ARG 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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317C ASN* 4.4 6.0 + - - +
318C ARG 2.7 30.1 + - - -
319C ALA* 3.0 19.6 + - - +
320C GLY* 3.7 25.8 - - - +
397C LEU* 3.4 27.8 - - - +
401C SER* 4.4 13.7 - - - -
409C GLU* 3.3 23.2 + - - -
438C HIS 3.2 12.2 + - - +
439C GLN* 2.9 55.5 - - - +
440C VAL 3.2 1.0 - - - -
441C ALA* 1.3 75.6 - - - +
443C TYR* 1.3 72.8 + - + +
444C ARG* 3.3 7.9 + - - +
465C TYR* 6.1 0.2 - - - -
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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