Contacts of the helix formed by residues 797 - 804 (chain B) in PDB entry 5V4R
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 797 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943A ARG* 3.7 27.9 + - + +
944A LEU* 4.1 17.4 - - + +
795B MET 3.7 2.4 + - - -
796B GLN* 1.3 76.1 - - - +
798B PRO* 1.3 77.7 - - + +
799B SER* 2.8 32.7 + - - +
800B HIS* 2.8 17.6 + - + +
801B GLU 3.2 8.7 + - - -
816B TYR* 3.4 30.7 - + - -
834B GLU* 3.0 30.3 + - - -
837B THR* 3.4 17.7 + - - +
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Residues in contact with PRO 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796B GLN* 3.6 4.5 - - + +
797B HIS* 1.3 100.6 - - + +
799B SER* 1.3 61.7 + - - +
801B GLU* 3.2 11.7 + - + +
802B LEU* 2.9 29.2 + - - +
812B VAL* 4.6 13.2 - - + +
816B TYR* 3.9 32.8 - - + -
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Residues in contact with SER 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A LEU* 4.4 6.8 + - - +
797B HIS* 2.8 26.7 + - - +
798B PRO* 1.3 77.2 - - - +
800B HIS* 1.3 64.3 + - - +
802B LEU* 3.3 2.7 + - - +
803B LEU* 3.0 32.1 + - - +
816B TYR* 3.6 24.5 - - - -
837B THR* 4.5 4.3 + - - -
840B ARG* 4.4 14.1 + - - -
841B PHE* 4.2 22.2 - - - -
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Residues in contact with HIS 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943A ARG 5.5 0.7 - - - -
944A LEU 3.4 28.0 - - - +
945A GLU* 4.4 16.2 - - - -
796B GLN* 2.7 26.8 + - + +
797B HIS* 2.8 19.3 + - + +
799B SER* 1.3 83.5 + - - +
801B GLU* 1.3 61.3 + - - +
803B LEU* 3.3 15.9 + - + +
804B LYS* 3.3 49.1 + - + +
840B ARG* 6.0 0.7 - - - +
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Residues in contact with GLU 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796B GLN* 3.4 36.8 + - + +
797B HIS 3.2 3.3 + - - +
798B PRO* 3.2 11.9 + - - +
800B HIS* 1.3 78.0 - - - +
802B LEU* 1.3 63.4 + - - +
803B LEU 3.3 0.9 + - - -
804B LYS* 3.3 22.3 + - + +
807B GLY* 3.6 24.5 - - - +
809B THR* 5.2 2.3 + - - +
812B VAL* 4.0 31.2 - - + +
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Residues in contact with LEU 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B PRO 2.9 20.4 + - - +
799B SER 3.3 1.1 + - - +
801B GLU* 1.3 78.3 - - + +
803B LEU* 1.3 59.2 + - - +
804B LYS 3.9 3.7 - - - +
807B GLY 4.3 5.4 - - - +
808B PHE* 3.8 24.5 - - + +
809B THR 3.7 33.2 - - - +
812B VAL* 3.8 23.8 - - + -
813B TYR* 3.7 31.0 - - + +
816B TYR* 3.8 22.4 - - + -
841B PHE* 3.4 22.9 - - + -
845B PHE* 4.1 11.3 - - - -
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Residues in contact with LEU 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799B SER* 3.0 21.2 + - - +
800B HIS* 3.9 7.4 - - + +
801B GLU 3.2 0.8 - - - -
802B LEU* 1.3 75.1 - - - +
804B LYS* 1.3 65.6 + - - +
805B GLU 3.6 1.0 + - - -
840B ARG* 4.1 24.5 - - - +
841B PHE* 3.6 30.5 - - + -
844B PHE* 4.0 22.2 - - + -
845B PHE* 3.8 29.8 - - + +
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Residues in contact with LYS 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796B GLN* 3.3 19.1 - - - +
800B HIS* 3.3 45.5 + - + +
801B GLU* 3.3 13.9 + - + +
802B LEU 3.9 4.2 - - - +
803B LEU* 1.3 81.7 - - - +
805B GLU* 1.3 70.8 + - - +
806B ASN 3.3 0.7 + - - -
807B GLY* 3.0 17.9 + - - -
808B PHE* 4.2 0.7 + - - +
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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