Contacts of the strand formed by residues 1015 - 1019 (chain B) in PDB entry 4HPF
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 ARG1015 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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897B THR* 3.4 26.3 + - - -
1001B TYR* 3.0 64.8 + - + -
1002B ARG 3.1 13.5 - - - +
1003B ILE* 3.5 40.2 - - + +
1004B ILE* 4.3 2.9 - - - +
1013B ASN* 3.7 5.4 + - - +
1014B LYS* 1.3 74.3 - - - +
1016B PHE* 1.3 62.2 + - - +
1030B SER* 3.2 29.7 + - - -
1032B LEU* 3.4 28.5 - - - +
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Residues in contact with PHE1016 (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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513B TRP* 3.5 68.9 - + + -
516B HIS* 4.4 4.9 - + + -
517B PHE* 4.0 20.4 - + - -
896B SER* 3.5 14.1 - - - +
897B THR 4.7 0.2 - - - +
1001B TYR* 3.4 7.1 - - - -
1002B ARG* 2.7 76.0 + - + +
1003B ILE 3.8 8.5 - - - -
1004B ILE* 3.8 11.2 - - + -
1015B ARG* 1.3 73.9 - - - +
1017B VAL* 1.3 63.4 + - - +
1018B ILE* 3.5 35.2 + - + -
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Residues in contact with VAL1017 (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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491B GLY* 3.7 12.3 - - - +
494B THR* 3.3 23.6 - - - +
495B PHE* 3.7 33.7 - - + +
498B SER* 5.3 0.7 - - - +
517B PHE* 3.3 28.3 - - + -
520B SER* 3.9 4.5 + - - -
896B SER 3.2 9.5 + - - +
1000B LEU 3.8 2.9 - - - -
1001B TYR* 3.4 26.0 - - + -
1016B PHE* 1.3 73.7 - - - +
1018B ILE* 1.3 65.5 + - - +
1019B THR* 4.0 10.7 + - + -
1034B PHE* 3.9 11.0 - - + -
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Residues in contact with ILE1018 (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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516B HIS* 4.5 9.9 - - + +
520B SER* 4.1 13.7 - - - -
999B GLY* 3.3 4.2 - - - -
1000B LEU* 2.9 45.0 + - + +
1002B ARG* 3.9 25.6 - - + +
1016B PHE* 3.5 39.0 + - + +
1017B VAL* 1.3 71.6 - - - +
1019B THR* 1.3 66.3 + - - +
1020B ARG 3.7 0.2 + - - -
1021B PRO* 4.0 27.0 - - + +
1025B PHE* 4.1 19.3 - - + -
1034B PHE* 5.8 0.4 - - - -
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Residues in contact with THR1019 (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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495B PHE* 2.9 45.8 - - + -
498B SER* 3.3 21.5 + - - +
499B LEU* 4.5 10.3 - - + -
520B SER* 2.8 44.7 + - - -
523B ASN* 3.1 13.9 + - - +
589B ILE* 6.5 0.2 - - - -
998B VAL 4.5 2.2 - - - -
999B GLY* 4.5 1.3 - - - -
1017B VAL* 3.9 6.6 + - + +
1018B ILE* 1.3 73.9 - - - +
1020B ARG* 1.3 72.2 + - - +
1021B PRO* 3.4 0.5 - - - +
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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