Contacts of the helix formed by residues 699 - 707 (chain A) in PDB entry 4PE5
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 699 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A ILE* 5.1 5.4 - - + -
673A ARG* 4.4 11.9 - - - +
692A TYR* 4.7 11.2 - - + +
693A PHE* 3.3 52.9 - - + +
696A GLN* 3.4 52.6 + - + +
697A VAL 3.2 1.2 - - - -
698A GLU* 1.3 95.7 - - + +
700A SER* 1.3 62.3 + - - +
701A THR 3.6 1.3 - - - -
702A MET* 3.6 22.8 - - + +
703A TYR* 3.4 11.6 + - - +
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Residues in contact with SER 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A PHE 5.0 0.2 - - - -
694A ARG 5.9 0.7 - - - -
696A GLN 3.6 6.3 + - - -
697A VAL* 3.7 15.7 - - - -
698A GLU 3.5 2.2 - - - -
699A LEU* 1.3 75.7 - - - +
701A THR* 1.3 58.2 + - - +
703A TYR* 2.9 10.2 + - - +
704A ARG* 2.7 35.8 + - - +
431B ARG* 5.9 8.5 - - - -
432B ASN* 5.9 6.3 - - - -
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Residues in contact with THR 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A ARG 3.9 21.1 - - - +
674A ASN* 5.0 5.7 + - - +
675A PRO* 4.1 15.0 - - + -
698A GLU 5.4 0.4 + - - -
699A LEU 3.6 0.2 - - - -
700A SER* 1.3 77.2 - - - +
702A MET* 1.3 65.0 + - - +
704A ARG* 2.9 11.9 + - + +
705A HIS* 2.8 21.0 + - + +
431B ARG* 5.2 7.5 - - - +
432B ASN* 4.0 18.7 + - - -
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Residues in contact with MET 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A ILE* 3.6 24.2 - - + +
672A LEU* 3.4 34.8 - - + +
673A ARG* 3.6 33.4 - - - +
675A PRO* 5.3 0.2 - - - -
681A TYR* 3.3 24.5 - - + +
693A PHE* 3.5 34.1 - - + -
699A LEU* 3.6 20.3 + - + +
700A SER 3.3 0.4 - - - -
701A THR* 1.3 78.7 - - - +
703A TYR* 1.3 51.1 + - - +
705A HIS* 2.9 5.9 + - - +
706A MET* 2.7 40.4 + - - +
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Residues in contact with TYR 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A ASP* 3.1 41.5 + - - -
693A PHE* 3.4 35.1 - - + +
694A ARG* 3.7 25.5 - - + +
699A LEU 3.4 13.2 + - - +
700A SER* 2.9 10.9 + - - +
702A MET* 1.3 77.9 - - - +
704A ARG* 1.3 59.5 + - + +
706A MET* 2.9 7.7 + - + +
707A GLU* 2.7 56.3 + - + +
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Residues in contact with ARG 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A SER 2.7 16.1 + - - +
701A THR* 2.9 14.3 + - + +
703A TYR* 1.3 77.2 - - + +
705A HIS* 1.3 57.2 + - - +
707A GLU* 4.3 8.1 + - - +
708A LYS* 4.7 8.3 - - - +
194B PHE* 6.2 4.5 - - + -
431B ARG* 5.7 8.7 - - + -
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Residues in contact with HIS 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A PRO* 3.5 29.2 - - + +
676A SER* 3.4 23.8 + - - -
679A PHE 3.4 20.2 + - - -
680A ILE* 3.7 11.7 - - + +
681A TYR* 3.3 45.1 + + - -
701A THR 2.8 10.7 + - - +
702A MET* 2.9 9.4 + - - +
704A ARG* 1.3 79.0 - - - +
706A MET* 1.3 59.1 + - - +
707A GLU 3.5 0.2 - - - -
708A LYS* 4.0 3.1 + - - +
709A HIS* 3.1 35.1 + + - -
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Residues in contact with MET 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A TYR* 3.9 32.1 - - + +
682A ALA* 4.0 20.2 - - - -
683A THR* 3.7 19.7 - - + -
689A VAL* 4.4 1.3 - - + +
690A ASP* 5.2 2.0 - - - +
693A PHE* 3.4 46.9 - - + -
702A MET 2.7 16.9 + - - +
703A TYR* 2.9 8.9 + - + +
705A HIS* 1.3 75.6 - - - +
707A GLU* 1.3 51.6 + - - +
708A LYS 2.7 17.2 + - - -
709A HIS 3.1 8.0 + - - -
710A ASN* 3.0 31.4 + - - +
730A ILE* 4.3 16.8 - - - -
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Residues in contact with GLU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A ASP* 5.6 0.4 - - - +
703A TYR* 2.7 44.0 + - + +
704A ARG* 4.8 5.8 - - - +
705A HIS 3.5 0.6 - - - -
706A MET* 1.3 70.7 - - - +
708A LYS* 1.3 58.4 + - - +
710A ASN* 3.8 12.8 - - - +
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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