Contacts of the helix formed by residues 591 - 601 (chain C) in PDB entry 2V4M
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 591 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563C ARG* 3.6 26.6 - - - +
589C LEU* 3.2 4.9 - - - +
590C ALA* 1.3 77.1 - - - +
592C GLU* 1.3 58.4 + - - +
593C LEU 3.4 0.4 - - - -
594C LYS* 3.4 23.8 + - - +
595C HIS* 3.6 12.6 + - - -
420D SER* 3.7 25.0 + - - -
446D ASP* 4.6 0.3 - - - +
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Residues in contact with GLU 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C ILE* 5.2 1.1 - - + -
589C LEU* 2.9 30.1 + - + +
591C GLY* 1.3 77.8 - - - +
593C LEU* 1.3 63.8 + - - +
594C LYS 3.3 2.9 - - - -
595C HIS* 3.0 27.6 + - - +
597C PRO* 3.4 21.3 - - + +
392D CYS* 3.4 15.8 - - - +
393D GLY* 2.8 40.8 + - - -
418D LEU* 3.3 31.4 - - + +
419D ALA 5.2 0.2 + - - -
420D SER* 4.3 4.2 + - - +
575D LEU* 5.6 0.7 - - - +
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Residues in contact with LEU 593 (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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561C MET* 3.4 44.0 - - + -
588C ILE* 4.1 18.6 - - + -
589C LEU 3.6 1.8 + - - -
590C ALA* 3.2 24.2 + - - +
592C GLU* 1.3 76.1 - - - +
594C LYS* 1.3 59.3 + - - +
595C HIS 3.1 4.9 + - - -
596C GLY 3.4 4.5 + - - -
597C PRO* 3.6 7.4 - - + +
598C LEU* 3.1 58.9 + - + +
623C ALA* 4.1 21.8 - - + +
626C GLN* 4.5 8.5 - - + +
627C VAL* 4.2 10.5 - - + -
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Residues in contact with LYS 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C ARG* 5.1 4.6 - - - +
590C ALA 4.9 1.2 + - - -
591C GLY* 3.4 24.1 + - - +
593C LEU* 1.3 76.8 - - - +
595C HIS* 1.3 84.9 + - + +
596C GLY 3.4 2.7 + - - -
598C LEU* 4.9 5.2 - - + -
626C GLN* 3.6 33.9 + - - +
446D ASP* 4.1 14.3 + - - +
800D F6R 5.1 0.3 + - - -
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Residues in contact with HIS 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C GLY 3.6 19.1 + - - -
592C GLU* 3.0 30.5 + - - +
594C LYS* 1.3 103.1 + - + +
596C GLY* 1.3 54.8 + - - +
597C PRO* 3.5 6.2 - - - +
392D CYS* 3.4 31.5 - - + +
393D GLY* 4.2 0.4 - - - -
444D THR* 3.8 24.2 - - + -
446D ASP* 4.8 3.8 + - - -
575D LEU* 3.9 5.2 - - - +
579D GLU* 4.7 1.8 - - - -
800D F6R 2.7 64.7 + - - +
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Residues in contact with GLY 596 (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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593C LEU 3.4 2.4 + - - -
594C LYS 3.4 2.6 + - - -
595C HIS* 1.3 80.1 - - - +
597C PRO* 1.3 65.8 - - - +
598C LEU* 3.2 4.7 + - - +
599C ALA* 3.2 22.6 + - - +
575D LEU* 3.9 11.2 - - - -
578D LYS 4.8 0.2 - - - -
579D GLU* 3.9 26.6 + - - +
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Residues in contact with PRO 597 (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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559C LEU* 5.1 2.4 - - - +
588C ILE* 4.3 21.5 - - + +
592C GLU* 3.4 26.9 - - + +
593C LEU* 3.7 17.5 - - + +
595C HIS 3.5 2.7 - - - -
596C GLY* 1.3 90.5 - - - +
598C LEU* 1.3 60.8 + - - +
599C ALA 3.1 0.2 - - - -
600C LEU* 3.0 24.1 + - - +
601C VAL* 4.3 2.4 + - - +
575D LEU* 3.7 16.2 - - + -
578D LYS* 4.2 24.7 - - + +
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Residues in contact with LEU 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C LEU* 3.1 32.9 + - + +
594C LYS* 4.9 3.4 - - - -
596C GLY 3.2 1.3 + - - +
597C PRO* 1.3 75.7 - - - +
599C ALA* 1.3 57.3 + - - +
601C VAL* 2.8 33.3 + - + +
626C GLN* 3.6 55.2 - - + +
627C VAL* 4.3 15.7 - - + +
630C ARG* 3.8 40.2 + - + +
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Residues in contact with ALA 599 (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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596C GLY 3.2 15.0 + - - +
597C PRO 3.1 0.2 - - - -
598C LEU* 1.3 77.9 - - - +
600C LEU* 1.3 60.0 + - - +
601C VAL 3.3 5.5 + - - +
630C ARG* 3.7 15.8 + - - +
578D LYS 4.0 4.0 - - - +
579D GLU* 3.4 26.5 - - + +
582D TYR* 3.4 30.5 - - + +
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Residues in contact with LEU 600 (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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559C LEU* 4.4 16.6 - - + -
588C ILE* 5.7 0.4 - - + -
597C PRO 3.0 14.0 + - - +
598C LEU 2.9 1.0 + - - -
599C ALA* 1.3 79.4 - - - +
601C VAL* 1.3 60.0 + - - +
602C ASP* 3.6 8.1 + - - +
605C MET* 3.7 26.9 - - + +
578D LYS* 3.7 36.2 + - + +
582D TYR* 3.3 27.8 - - + +
583D MET 3.3 22.9 - - - +
584D HIS* 3.8 29.2 - - + +
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Residues in contact with VAL 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C LEU* 4.1 10.1 - - + -
561C MET* 3.8 29.2 - - + -
597C PRO 4.8 0.7 - - - +
598C LEU* 2.8 30.6 + - + +
599C ALA 4.2 4.6 - - - +
600C LEU* 1.3 78.2 - - - +
602C ASP* 1.3 66.6 + - - +
605C MET* 4.4 3.8 - - - -
607C VAL* 4.3 8.7 - - + -
627C VAL* 3.9 26.5 - - + +
630C ARG* 3.7 34.5 - - + +
632C GLY* 4.1 10.3 - - - -
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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