Contacts of the helix formed by residues 541 - 551 (chain D) 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 MET 541 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537D GLU* 3.6 25.6 - - + +
538D VAL* 3.1 18.7 + - - +
540D SER* 1.3 76.6 - - - +
542D ASP* 1.3 64.0 + - - +
543D ASP 3.3 2.7 - - - -
544D GLU* 3.1 33.5 + - - +
545D ILE* 3.0 31.7 + - + +
640D LYS* 5.5 2.0 - - + -
653D ILE* 4.5 8.1 - - + -
654D LYS 2.9 33.0 - - - +
655D VAL* 3.8 10.1 - - - -
656D PRO* 3.8 23.3 - - + -
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Residues in contact with ASP 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D GLN* 4.5 5.9 + - - -
348D PHE* 4.1 22.3 - - + -
538D VAL 4.2 0.4 + - - -
539D LEU 3.1 18.7 + - - +
540D SER 3.2 1.8 - - - -
541D MET* 1.3 78.3 - - - +
543D ASP* 1.3 59.0 + - - +
545D ILE* 3.1 8.0 + - - +
546D GLN* 2.8 34.5 + - - +
673D LEU* 3.8 16.7 - - + +
677D HIS* 2.5 39.2 + - - -
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Residues in contact with ASP 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D SER 4.6 6.0 + - - +
541D MET 3.3 0.8 - - - -
542D ASP* 1.3 81.6 - - - +
544D GLU* 1.3 63.2 + - + +
546D GLN* 3.4 16.5 + - - +
547D LYS* 3.0 22.9 + - - +
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Residues in contact with GLU 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541D MET* 3.1 37.6 + - + +
543D ASP* 1.3 77.9 - - + +
545D ILE* 1.3 61.4 + - + +
547D LYS* 3.2 12.0 + - - +
548D LEU* 3.0 25.3 + - - +
651D ARG* 4.6 4.6 + - - +
653D ILE* 5.4 7.8 - - + +
654D LYS* 5.2 16.3 + - - +
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Residues in contact with ILE 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D VAL 4.5 2.7 - - - +
541D MET* 3.0 34.8 + - + +
542D ASP* 3.1 6.5 + - - +
544D GLU* 1.3 75.4 - - + +
546D GLN* 1.3 61.8 + - - +
548D LEU* 3.3 8.2 + - + +
549D ALA* 3.0 26.9 + - - +
653D ILE* 4.1 27.6 - - + -
670D PRO* 3.7 44.6 - - + +
673D LEU* 4.1 20.6 - - + +
674D LEU* 3.8 24.4 - - + +
677D HIS* 4.5 1.8 - - + -
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Residues in contact with GLN 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542D ASP* 2.8 17.8 + - - +
543D ASP* 3.5 16.9 - - - +
545D ILE* 1.3 77.2 - - - +
547D LYS* 1.3 61.8 + - - +
549D ALA* 3.2 12.5 + - - +
550D THR* 3.3 19.4 + - + +
677D HIS* 3.5 44.6 + - + +
680D VAL* 6.1 2.4 - - - +
681D LEU* 4.5 2.8 - - + +
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Residues in contact with LYS 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D ASP 3.0 13.8 + - - +
544D GLU* 3.3 13.9 - - - +
546D GLN* 1.3 76.9 - - - +
548D LEU* 1.3 61.3 + - - +
550D THR* 2.4 31.5 + - - +
551D GLU* 3.6 10.4 + - - +
651D ARG* 3.4 27.8 - - - +
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Residues in contact with LEU 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D GLU 3.0 11.5 + - - +
545D ILE* 3.5 9.6 - - - +
547D LYS* 1.3 76.4 - - - +
549D ALA* 1.3 62.1 + - - +
551D GLU* 3.0 26.0 + - + +
552D LEU* 3.4 22.7 + - + +
608D ILE* 5.6 1.1 - - + -
635D VAL* 3.8 37.5 - - + -
651D ARG* 4.0 25.5 - - - +
653D ILE* 3.6 33.0 - - + -
674D LEU* 4.3 18.4 - - + -
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Residues in contact with ALA 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D ILE 3.0 13.3 + - - +
546D GLN 3.2 10.3 + - - +
548D LEU* 1.3 77.0 - - - +
550D THR* 1.3 55.6 + - - +
552D LEU 3.0 0.9 + - - -
553D TYR 3.0 27.0 + - - -
674D LEU* 3.7 9.8 - - + +
677D HIS* 3.8 16.4 - - + -
678D LEU* 3.3 28.7 - - + +
681D LEU* 3.5 15.8 - - + +
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Residues in contact with THR 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D GLN* 3.3 17.8 + - + +
547D LYS* 2.4 29.3 + - - +
549D ALA* 1.3 75.7 - - - +
551D GLU* 1.3 61.2 + - - +
552D LEU 3.5 0.5 + - - -
553D TYR* 3.5 20.7 - - - -
554D HIS* 4.8 3.3 + - - -
681D LEU* 3.7 27.8 - - + -
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Residues in contact with GLU 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D LYS* 4.0 12.8 - - + +
548D LEU* 3.0 17.2 + - + +
550D THR* 1.3 80.3 - - - +
552D LEU* 1.3 62.0 + - + +
554D HIS* 3.3 21.5 - - - -
555D GLN* 4.7 1.6 + - - +
650D LYS* 5.1 8.5 + - - -
651D ARG* 3.2 46.6 + - - +
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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