Contacts of the helix formed by residues 505 - 513 (chain C) in PDB entry 1P4V
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 HIS 505 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443C PRO* 3.0 32.0 + - + -
444C ILE* 4.9 0.4 - - - -
445C VAL* 3.6 23.2 - - + +
473C MET* 3.6 17.7 - - + -
504C GLY* 1.3 67.2 - - - -
506C GLY* 1.3 66.5 + - - +
507C GLU* 3.3 6.7 - - + +
508C GLU* 3.0 32.2 + - + +
509C VAL* 3.6 4.9 + - - +
552C ASP 3.2 24.5 + - - -
553C ILE* 3.5 7.4 - - + -
554C GLN* 2.8 38.7 + - + +
555C VAL* 4.0 4.7 - - - +
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Residues in contact with GLY 506 (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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473C MET* 3.9 0.2 - - - +
480C ARG* 4.2 0.9 - - - -
483C ASP* 3.1 35.4 - - - +
504C GLY 2.9 9.1 + - - -
505C HIS* 1.3 70.3 - - - +
507C GLU* 1.3 65.8 + - - +
509C VAL* 2.9 4.8 + - - +
510C ILE* 2.9 26.9 + - - +
596C GLY* 2.9 13.5 + - - -
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Residues in contact with GLU 507 (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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100A PRO 3.5 22.4 - - - +
101A HIS* 3.1 20.0 + - - +
102A VAL* 3.7 39.3 + - + +
441C TYR* 5.9 0.4 - - - -
473C MET* 4.5 4.9 - - - +
480C ARG* 2.9 39.3 + - - +
481C VAL 4.7 3.3 - - - +
482C GLY* 5.4 0.2 - - - -
505C HIS* 3.2 6.0 + - + +
506C GLY* 1.3 74.9 + - - +
508C GLU* 1.3 68.9 + - + +
510C ILE* 3.5 2.9 + - - +
511C ARG* 3.0 32.4 + - - +
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Residues in contact with GLU 508 (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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505C HIS* 3.0 16.2 + - + +
507C GLU* 1.3 79.8 - - + +
509C VAL* 1.3 61.6 + - - +
511C ARG* 2.9 45.8 + - - +
512C THR* 3.0 30.7 + - - +
539C ILE* 3.9 14.9 - - + +
542C ILE* 5.1 2.1 - - - +
543C VAL* 4.2 11.3 - - - +
546C ARG* 4.1 8.1 + - - -
553C ILE* 3.4 40.0 - - + +
555C VAL* 4.2 12.3 - - + -
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Residues in contact with VAL 509 (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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483C ASP* 3.4 24.5 - - + +
489C ALA* 3.2 31.0 - - - +
502C ALA* 3.9 12.8 - - + -
503C THR 4.6 4.3 - - - +
505C HIS 4.1 5.4 - - - +
506C GLY* 2.9 8.4 + - - +
508C GLU* 1.3 74.5 - - - +
510C ILE* 1.3 59.9 + - - +
512C THR* 4.0 4.3 - - - -
513C VAL* 2.9 24.6 + - - -
514C GLY* 3.0 18.1 + - - +
539C ILE* 4.7 1.3 - - + -
555C VAL* 3.6 36.3 - - + -
557C PHE* 4.3 2.2 - - + -
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Residues in contact with ILE 510 (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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76A ILE* 3.7 19.1 - - + -
102A VAL* 3.6 21.1 - - + -
103A MET* 4.9 2.9 - - + -
187A ILE* 3.7 30.9 - - + +
481C VAL 4.0 4.3 - - - +
482C GLY* 3.4 32.5 - - - +
483C ASP* 3.7 15.5 - - - +
486C ILE* 3.8 20.6 - - + -
489C ALA* 4.2 9.4 - - + +
506C GLY 2.9 15.2 + - - +
507C GLU* 3.7 6.3 - - - +
509C VAL* 1.3 77.6 - - - +
511C ARG* 1.3 62.8 + - - +
513C VAL* 3.1 12.8 + - - +
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Residues in contact with ARG 511 (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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70A MET* 5.4 2.6 - - - +
74A TYR* 2.8 47.5 + - + +
75A ASN* 3.9 0.6 - - - +
76A ILE* 3.6 34.6 - - + +
102A VAL* 4.0 16.3 - - - +
187A ILE* 4.6 2.7 - - - +
192A PHE* 3.9 18.2 - - - -
507C GLU* 3.0 19.8 + - - +
508C GLU* 2.9 44.5 + - - +
510C ILE* 1.3 79.3 - - - +
512C THR* 1.3 59.9 + - + +
542C ILE* 3.6 29.8 - - + +
546C ARG* 3.4 29.9 - - - +
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Residues in contact with THR 512 (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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192A PHE* 5.0 2.7 - - - -
216A HIS* 4.0 11.5 - - - -
508C GLU* 3.0 19.5 + - - +
509C VAL* 3.6 4.5 + - - -
510C ILE 3.2 0.6 - - - -
511C ARG* 1.3 79.7 - - + +
513C VAL* 1.3 75.4 + - - +
514C GLY* 3.0 10.3 + - - -
517C LEU* 4.2 10.1 - - - +
535C ALA 5.5 0.4 - - - -
538C ARG* 4.8 9.3 + - + -
539C ILE* 3.5 31.9 - - + +
542C ILE* 3.3 34.5 - - + -
557C PHE* 4.9 0.3 - - - -
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Residues in contact with VAL 513 (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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187A ILE 3.8 18.4 - - - +
188A GLY* 4.0 1.8 - - - -
192A PHE* 3.6 31.6 - - + -
213A VAL* 3.5 31.2 - - + -
216A HIS* 3.7 17.7 - - + +
487C ILE 5.4 0.4 - - - +
488C GLY 3.0 30.6 - - - +
489C ALA* 4.5 2.7 - - + +
509C VAL 2.9 8.4 + - - -
510C ILE 3.1 12.6 + - - +
512C THR* 1.3 80.4 - - - +
514C GLY* 1.3 64.3 + - - +
516C HIS* 3.9 1.8 - - + -
517C LEU* 3.1 15.8 + - - +
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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