Contacts of the helix formed by residues 513 - 524 (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 VAL 513 (chain C).
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Specific contacts
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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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Residues in contact with GLY 514 (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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488C GLY 3.7 0.6 + - - -
509C VAL* 3.0 13.5 + - - +
512C THR* 3.0 11.4 - - - -
513C VAL* 1.3 74.7 - - - +
515C THR* 1.3 57.5 + - - +
517C LEU* 3.1 8.2 + - - +
518C VAL* 2.9 28.9 + - - +
535C ALA* 4.5 1.7 - - - +
557C PHE* 3.6 28.4 - - - -
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Residues in contact with THR 515 (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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488C GLY 3.1 14.5 + - - -
489C ALA 2.6 24.8 + - - +
490C GLY 3.7 2.9 - - - +
491C LEU 3.2 11.6 - - - -
492C PHE* 3.7 5.6 - - - -
500C ALA* 3.4 32.8 - - + +
501C THR* 3.5 24.5 - - - +
502C ALA* 3.8 5.4 - - + +
514C GLY* 1.3 70.8 - - - +
516C HIS* 1.3 64.1 + - - +
518C VAL* 3.7 6.3 - - - +
519C VAL* 3.0 28.1 + - - +
557C PHE* 4.2 3.4 - - + -
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Residues in contact with HIS 516 (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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212A THR 4.1 7.9 - - - -
213A VAL* 3.7 21.7 - - + +
216A HIS* 2.9 32.3 - + + -
217A LEU* 4.0 29.1 - - + +
220A GLU* 6.0 0.2 - - + -
488C GLY* 3.0 26.9 + - - +
492C PHE* 3.7 35.0 - + - +
513C VAL* 3.6 9.4 - - + +
515C THR* 1.3 77.8 + - - +
517C LEU* 1.3 58.1 + - - +
519C VAL* 3.4 1.1 + - + +
520C GLU* 2.8 42.0 + - + +
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Residues in contact with LEU 517 (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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216A HIS* 3.9 13.8 + - - +
220A GLU* 4.1 12.3 - - + +
512C THR* 4.2 12.3 - - - +
513C VAL 3.1 11.5 + - - +
514C GLY* 3.1 9.7 + - - +
516C HIS* 1.3 78.2 - - - +
518C VAL* 1.3 57.8 + - - +
520C GLU* 3.2 4.3 + - + -
521C LEU* 2.8 55.6 + - + +
534C GLU 5.0 0.2 - - - +
535C ALA* 3.9 25.4 - - + +
538C ARG* 3.7 57.2 - - + +
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Residues in contact with VAL 518 (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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500C ALA* 3.7 20.4 - - + -
514C GLY 2.9 19.8 + - - +
515C THR* 3.7 6.3 - - - +
516C HIS 3.3 0.4 - - - -
517C LEU* 1.3 75.5 - - - +
519C VAL* 1.3 57.9 + - - +
521C LEU* 3.2 1.4 + - - -
522C MET* 3.0 25.9 + - + +
531C ALA* 3.4 32.2 - - + +
532C CYS* 4.1 7.2 - - - -
535C ALA* 3.5 23.1 - - + -
557C PHE* 4.1 21.8 - - + -
559C ALA* 3.8 17.3 - - + -
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Residues in contact with VAL 519 (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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492C PHE* 3.7 48.9 - - + +
494C ASP* 4.0 7.2 - - + -
497C ILE* 3.4 26.2 - - + +
498C GLY 3.9 17.3 - - - +
500C ALA* 4.0 12.1 - - + +
515C THR 3.0 17.9 + - - +
516C HIS 3.9 0.7 - - - +
518C VAL* 1.3 76.6 - - - +
520C GLU* 1.3 58.8 + - - +
522C MET* 3.2 13.0 + - + -
523C ASN* 2.8 24.3 + - - +
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Residues in contact with GLU 520 (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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217A LEU* 4.3 8.3 - - + +
220A GLU* 3.7 22.4 - - + -
224A GLN* 3.2 18.6 + - - +
238A ARG* 3.3 18.9 + - - -
497C ILE* 5.3 1.6 - - - +
516C HIS* 2.8 32.8 + - + +
517C LEU* 3.7 7.4 - - + +
519C VAL* 1.3 77.3 - - - +
521C LEU* 1.3 58.1 + - - +
523C ASN* 3.1 30.4 + - - +
524C GLN* 2.9 40.6 + - - +
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Residues in contact with LEU 521 (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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220A GLU* 5.2 2.0 - - - +
517C LEU* 2.8 45.9 + - + +
518C VAL 3.6 4.7 - - - +
520C GLU* 1.3 73.2 - - - +
522C MET* 1.3 65.6 + - - +
524C GLN* 3.0 28.8 + - - +
525C GLY 3.2 0.5 + - - -
526C ARG* 3.0 50.6 + - - +
531C ALA* 3.5 31.9 - - + +
534C GLU* 3.7 23.6 - - + +
535C ALA 4.3 2.5 - - - +
538C ARG* 5.4 4.0 - - - +
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Residues in contact with MET 522 (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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497C ILE* 3.8 11.6 - - + +
498C GLY* 4.0 4.9 - - - -
499C ALA 3.7 22.0 - - - +
518C VAL* 3.0 14.5 + - + +
519C VAL* 3.5 25.1 - - + +
521C LEU* 1.3 73.8 - - - +
523C ASN* 1.3 65.1 + - - +
525C GLY* 2.9 13.9 + - - -
526C ARG 3.4 17.6 - - - +
528C PRO* 3.8 32.5 - - + -
531C ALA* 3.6 14.4 - - + -
559C ALA* 4.0 9.0 - - + -
560C LEU 3.7 21.8 - - - +
561C ASN* 4.1 9.6 - - + -
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Residues in contact with ASN 523 (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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238A ARG* 3.5 22.0 - - - +
497C ILE* 3.4 40.9 - - + +
519C VAL 2.8 9.3 + - - +
520C GLU* 3.1 34.5 + - - +
522C MET* 1.3 77.1 - - - +
524C GLN* 1.3 58.6 + - - +
525C GLY* 3.4 1.2 + - - -
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Residues in contact with GLN 524 (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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220A GLU* 3.3 14.0 + - - +
224A GLN* 2.8 39.5 + - - +
520C GLU* 2.9 31.5 + - - +
521C LEU* 3.0 24.8 + - - +
523C ASN* 1.3 77.7 - - - +
525C GLY* 1.3 55.9 + - - -
526C ARG* 3.6 30.0 + - - +
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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