Contacts of the strand formed by residues 554 - 558 (chain B) in PDB entry 2H5G
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 LEU 554 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B ILE* 4.1 24.2 - - + -
475B VAL 3.5 2.4 + - - -
476B LEU* 3.5 23.6 - - + +
477B LEU 2.8 26.9 + - - +
552B ILE* 3.3 3.4 - - - +
553B ASP* 1.3 80.9 - - - +
555B ILE* 1.3 76.4 + - - +
556B ILE* 4.0 23.5 + - + +
574B ILE* 4.1 0.4 - - - -
575B PRO* 3.3 32.3 - - + +
576B VAL 4.4 0.2 - - - -
577B MSE 3.8 35.7 - - + +
757B LEU* 4.5 4.7 - - + -
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Residues in contact with ILE 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LEU* 3.4 20.6 - - + +
479B ILE* 4.0 17.3 - - + -
552B ILE* 4.2 8.7 - - + -
554B LEU* 1.3 75.1 - - - +
556B ILE* 1.3 70.2 + - - +
557B PRO* 3.6 1.4 - - + +
567B ILE* 3.8 25.8 - - + -
571B ALA* 3.8 27.8 - - + -
574B ILE* 3.7 29.8 - - + -
575B PRO 2.9 11.1 + - - +
576B VAL* 3.3 6.2 - - + -
577B MSE 2.8 27.4 + - - -
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Residues in contact with ILE 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B LEU* 4.5 14.6 - - + -
477B LEU 2.7 12.2 + - - +
478B VAL* 3.4 27.8 - - + +
479B ILE 3.0 23.4 + - - +
554B LEU* 4.0 25.6 - - + +
555B ILE* 1.3 79.9 - - - +
557B PRO* 1.3 67.4 - - + +
558B ARG* 4.3 4.5 - - + -
577B MSE 3.9 19.1 - - + +
739B VAL* 3.3 50.5 - - + +
740B GLY* 5.2 1.1 - - - -
757B LEU* 4.4 7.9 - - + -
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Residues in contact with PRO 557 (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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479B ILE* 3.3 7.4 - - + +
555B ILE* 3.6 7.4 - - + +
556B ILE* 1.3 85.8 - - - +
558B ARG* 1.3 72.7 + - - +
559B GLY 4.1 0.4 - - - -
563B LEU* 5.1 1.1 - - + -
564B VAL* 4.3 32.6 - - + +
567B ILE* 3.5 29.8 - - + -
576B VAL* 3.7 22.7 - - + -
577B MSE 3.2 19.7 - - - +
578B GLY* 5.2 5.8 - - - -
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Residues in contact with ARG 558 (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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303B SO4 2.9 37.7 + - - -
478B VAL* 4.5 5.4 - - + -
479B ILE 2.7 9.3 + - - +
480B PHE* 3.3 19.8 - - + -
481B GLU* 3.0 26.5 + - - +
483B ARG* 3.8 20.1 + - - +
486B CYS* 3.9 25.0 - - - +
489B GLN* 6.0 1.4 - - - +
490B VAL* 4.6 2.0 - - - +
556B ILE* 4.3 10.1 - - + +
557B PRO* 1.3 83.2 - - - +
559B GLY* 1.3 56.9 + - - +
563B LEU* 3.9 2.6 - - - +
738B GLU* 3.7 21.8 + - - +
739B VAL* 2.8 43.0 + - - +
740B GLY* 3.8 15.2 - - - +
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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