Contacts of the helix formed by residues 698 - 707 (chain B) in PDB entry 4XUF
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 ASP 698 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B TYR 3.8 1.4 - - - +
697B GLY* 1.3 78.1 - - - +
699B LEU* 1.3 62.5 + - - +
700B LEU* 3.7 9.1 - - - +
701B ASN* 3.3 42.1 + - - +
702B TYR* 3.2 18.5 + - - +
814B ALA 4.4 1.1 - - - +
815B ARG* 4.0 22.1 - - - +
817B VAL 3.2 11.0 - - - +
818B LEU* 3.5 11.9 - - + +
830B PHE* 5.0 4.3 - - + -
1001B P30 5.1 5.3 - - + -
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Residues in contact with LEU 699 (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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698B ASP* 1.3 71.8 - - - +
700B LEU* 1.3 60.1 + - - +
702B TYR* 3.6 10.2 - - + +
703B LEU* 3.0 56.8 + - + +
791B PHE* 4.0 27.6 - - + -
795B VAL* 5.6 3.6 - - + -
814B ALA* 3.5 13.8 + - + +
817B VAL* 2.7 33.5 + - + +
819B VAL* 3.7 23.3 - - + -
825B VAL* 4.8 4.9 - - + -
877B LEU* 5.2 2.2 - - + -
881B ILE* 4.2 28.5 - - + -
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Residues in contact with LEU 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B ASP* 3.3 9.5 - - - +
699B LEU* 1.3 79.2 - - - +
701B ASN* 1.3 73.3 + - - +
703B LEU* 3.2 3.9 + - - +
704B ARG* 3.1 61.0 + - - +
814B ALA* 3.1 27.4 + - + +
815B ARG* 3.8 21.8 - - + +
839B ASP* 6.0 0.4 - - - +
841B ASN* 4.6 13.9 - - - +
880B GLU* 3.8 22.0 - - - +
885B GLY* 4.0 13.5 - - - +
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Residues in contact with ASN 701 (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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698B ASP* 3.3 29.3 + - - +
700B LEU* 1.3 88.3 - - - +
702B TYR* 1.3 57.7 + - - +
704B ARG* 4.0 9.9 - - - +
705B SER* 3.1 28.8 + - - -
1001B P30 6.4 2.0 - - - -
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Residues in contact with TYR 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B TYR* 4.2 40.1 + + + +
698B ASP 3.2 19.2 + - - +
699B LEU* 3.6 14.4 - - + +
700B LEU 3.2 0.8 - - - -
701B ASN* 1.3 80.1 - - - +
703B LEU* 1.3 77.2 + - + +
705B SER* 2.4 24.3 + - - -
706B LYS* 3.3 40.9 + - + +
781B ASN* 4.9 2.1 + - - -
783B LEU* 4.5 5.5 - - + +
791B PHE* 4.3 11.9 - + - -
819B VAL* 4.6 11.9 - - + -
823B LYS* 2.6 34.6 + - + +
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B LEU* 3.0 45.3 + - + +
700B LEU* 3.9 3.8 - - - +
702B TYR* 1.3 93.2 - - + +
704B ARG* 1.3 61.4 + - - +
705B SER 3.1 1.8 - - - -
706B LYS* 3.0 19.6 + - + +
707B ARG* 3.0 14.6 + - - +
783B LEU* 5.1 6.3 - - + -
788B LEU* 4.3 20.4 - - + -
791B PHE* 4.7 2.2 - - + -
814B ALA* 5.7 2.2 - - + -
880B GLU 3.6 23.3 - - - +
881B ILE* 4.0 17.5 - - + +
884B LEU* 3.9 27.7 - - + +
885B GLY* 4.2 1.3 - - - +
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Residues in contact with ARG 704 (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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700B LEU* 3.1 45.5 + - - +
701B ASN* 4.1 10.3 - - - +
703B LEU* 1.3 76.3 - - - +
705B SER* 1.3 60.1 + - - +
707B ARG* 3.5 33.0 + - - +
841B ASN* 5.5 4.9 + - - +
880B GLU* 5.1 1.2 + - - -
884B LEU 4.0 4.9 - - - -
885B GLY* 2.5 34.0 + - - +
886B VAL* 4.3 0.6 - - - -
887B ASN* 3.8 25.8 - - - +
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Residues in contact with SER 705 (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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701B ASN 3.1 14.4 + - - -
702B TYR* 2.4 35.6 + - - -
704B ARG* 1.3 78.7 - - - +
706B LYS* 1.3 66.0 + - - +
707B ARG 3.6 2.6 + - - -
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Residues in contact with LYS 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B TYR* 3.3 45.5 + - + +
703B LEU* 3.0 11.9 + - + +
705B SER* 1.3 81.6 + - - +
707B ARG* 1.3 61.3 + - - +
781B ASN* 2.9 48.2 + - - +
783B LEU* 4.1 21.1 - - + -
884B LEU* 4.5 11.9 - - + +
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Residues in contact with ARG 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU 3.0 9.8 + - - +
704B ARG* 3.5 32.0 + - - +
705B SER 3.3 3.3 - - - -
706B LYS* 1.3 81.6 - - - +
883B SER 4.2 4.5 - - - -
884B LEU* 2.7 49.8 + - + +
885B GLY 3.4 24.5 + - - -
886B VAL* 3.8 19.4 - - - +
913B TYR* 5.3 6.7 - - - +
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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