Contacts of the helix formed by residues 669 - 674 (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 ASP 669 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A ILE* 4.4 5.4 - - - -
665A THR* 3.7 27.1 - - + +
666A GLY 3.5 16.7 + - - +
667A ILE 3.2 2.4 - - - +
668A ASN* 1.3 77.9 - - - +
670A PRO* 1.3 64.7 - - + +
671A ARG* 3.1 8.3 - - + +
672A LEU* 3.0 35.1 + - + +
673A ARG* 3.2 11.4 + - - +
800B ILE* 5.6 2.7 - - + -
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Residues in contact with PRO 670 (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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665A THR* 4.6 7.9 - - + -
668A ASN 3.6 6.3 - - - +
669A ASP* 1.3 86.2 - - + +
671A ARG* 1.3 60.0 + - - +
672A LEU 3.1 1.6 + - - -
673A ARG* 3.8 11.4 - - + +
674A ASN* 3.4 23.9 + - - +
795B LEU 6.0 1.1 - - - +
798B THR* 3.8 43.1 - - - +
799B GLY 4.1 14.4 - - - +
800B ILE* 4.5 15.0 - - + +
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Residues in contact with ARG 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ILE* 6.3 2.0 - - + -
669A ASP* 3.1 4.1 - - + -
670A PRO* 1.3 78.1 - - - +
672A LEU* 1.3 70.0 + - + +
674A ASN 5.2 0.9 - - - -
675A PRO* 3.9 10.7 - - - +
679A PHE* 3.9 28.4 - - + +
681A TYR* 3.9 7.6 - - - -
800B ILE* 4.8 17.2 - - + +
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Residues in contact with LEU 672 (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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540A ILE* 4.1 25.4 - - + -
664A ILE* 4.9 11.2 - - + -
666A GLY 4.6 4.9 - - - +
667A ILE* 4.6 7.4 - - + +
669A ASP* 3.0 24.6 + - + +
671A ARG* 1.3 89.7 - - + +
673A ARG* 1.3 63.9 + - - +
674A ASN 3.4 1.6 - - - -
675A PRO* 3.4 5.4 - - - +
681A TYR* 2.4 60.9 + - + +
693A PHE* 6.4 0.4 - - + -
702A MET* 3.4 22.9 - - + +
728A ALA* 5.1 7.4 - - + -
730A ILE* 4.2 9.6 - - + -
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Residues in contact with ARG 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A ILE* 3.7 20.0 + - - +
668A ASN* 2.9 34.9 + - - +
669A ASP 3.2 18.3 + - - +
670A PRO* 4.1 9.0 - - + +
672A LEU* 1.3 79.5 - - - +
674A ASN* 1.3 69.1 + - - +
675A PRO* 3.4 5.2 - - - +
698A GLU* 4.4 10.3 + - - +
699A LEU* 4.4 15.4 - - - +
701A THR* 3.9 12.3 - - - +
702A MET* 3.6 27.2 - - + +
794B ALA 5.8 3.1 - - - +
795B LEU* 4.3 37.2 - - + +
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Residues in contact with ASN 674 (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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670A PRO 3.4 15.0 + - - +
671A ARG* 4.8 1.0 - - - +
673A ARG* 1.3 86.6 + - - +
675A PRO* 1.3 67.8 - - - +
676A SER* 5.0 1.2 - - - -
701A THR* 5.0 6.8 + - - +
418B ILE* 5.8 4.5 - - + -
738B TYR* 6.1 1.3 - - - +
795B LEU* 3.2 22.4 - - - +
796B TRP* 3.2 50.8 - - + +
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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