Contacts of the strand formed by residues 996 - 1003 (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 LEU 996 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539B PHE* 3.5 28.0 - - + -
543B ALA* 5.1 1.8 - - + -
553B LEU* 3.7 29.6 - - + -
554B LEU 3.7 10.8 - - - +
555B ILE* 3.9 19.1 - - + +
572B LEU* 6.1 0.4 - - + -
573B ASN* 3.5 34.1 - - + +
986B PHE* 3.8 12.8 - - + -
990B LEU* 4.6 9.2 - - + -
994B GLY 4.0 1.2 + - - -
995B ILE* 1.3 70.3 - - - +
997B CYS* 1.3 66.8 + - - +
998B VAL* 3.4 6.2 + - + +
1035B CYS* 3.3 2.5 - - - -
1036B ALA* 3.0 33.9 + - + +
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Residues in contact with CYS 997 (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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553B LEU* 4.1 2.8 - - - +
973B LEU* 4.6 7.2 - - - -
982B PHE* 3.8 15.9 - - + -
985B LEU* 4.6 11.9 - - + -
986B PHE* 3.2 41.8 - - + +
989B SER* 3.6 25.6 - - - -
995B ILE* 3.4 7.7 + - - -
996B LEU* 1.3 72.9 - - - +
998B VAL* 1.3 59.9 + - - +
999B GLY 3.9 0.2 - - - -
1033B VAL* 3.7 25.4 - - + -
1034B PHE 3.7 3.8 - - - -
1035B CYS* 3.7 9.4 - - - -
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Residues in contact with VAL 998 (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* 3.6 26.9 - - + -
553B LEU* 3.9 11.1 - - + +
555B ILE* 4.5 9.2 - - + -
589B ILE* 3.4 31.9 - - + -
963B LEU* 4.3 13.9 - - + -
982B PHE* 4.5 4.0 - - - -
996B LEU* 4.0 8.5 - - + +
997B CYS* 1.3 75.6 - - - +
999B GLY* 1.3 62.4 + - - +
1020B ARG* 3.1 23.9 + - - +
1034B PHE 2.9 23.5 + - - +
1035B CYS* 3.7 7.4 - - - +
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Residues in contact with GLY 999 (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* 4.6 2.0 - - - -
982B PHE* 4.5 2.3 - - - -
997B CYS 3.9 0.2 - - - -
998B VAL* 1.3 80.5 - - - +
1000B LEU* 1.3 63.9 + - - -
1018B ILE 3.3 12.8 - - - -
1019B THR* 4.5 1.6 - - - -
1020B ARG 4.1 3.1 - - - -
1021B PRO* 4.4 4.5 - - - -
1033B VAL* 3.4 7.3 - - - +
1034B PHE* 2.6 43.7 + - - +
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Residues in contact with LEU1000 (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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982B PHE* 4.2 15.0 - - + -
985B LEU* 5.5 0.4 - - + -
999B GLY* 1.3 77.1 - - - +
1001B TYR* 1.3 63.2 + - - +
1002B ARG* 4.0 17.9 - - + +
1018B ILE* 2.9 41.0 + - + +
1021B PRO* 4.2 20.9 - - + -
1025B PHE* 4.2 7.2 - - + -
1027B LEU* 3.6 31.6 - - + -
1031B ASP* 4.2 10.5 - - + +
1032B LEU 3.4 5.2 - - - +
1033B VAL* 3.4 30.1 - - + -
1034B PHE* 3.3 15.5 - - - -
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Residues in contact with TYR1001 (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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490B PRO* 4.1 17.0 - - + +
491B GLY* 4.0 12.7 + - - -
897B THR* 2.9 23.9 + - - -
965B LEU* 3.5 26.5 - - + -
1000B LEU* 1.3 73.7 - - - +
1002B ARG* 1.3 59.0 + - - +
1015B ARG* 3.0 73.3 + - + +
1016B PHE* 3.4 12.8 - - - -
1017B VAL* 3.4 30.1 - - + -
1031B ASP* 4.9 0.2 - - - -
1032B LEU* 2.8 26.3 + - + +
1034B PHE* 3.8 12.3 - + + -
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Residues in contact with ARG1002 (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* 6.3 0.2 - - - -
516B HIS* 5.3 7.2 + - - -
1000B LEU* 4.0 6.3 - - + +
1001B TYR* 1.3 74.1 - - - +
1003B ILE* 1.3 72.2 + - - +
1015B ARG* 3.1 2.1 - - - -
1016B PHE* 2.7 66.5 + - + -
1018B ILE* 3.9 17.6 - - + +
1025B PHE* 3.5 19.1 - - - -
1026B LYS 2.9 26.6 + - - -
1027B LEU* 3.8 2.6 - - - +
1028B LEU* 3.1 45.2 - - + +
1031B ASP* 3.1 42.1 + - - +
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Residues in contact with ILE1003 (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* 5.8 0.2 - - - +
1002B ARG* 1.3 91.4 - - - +
1004B ILE* 1.3 77.7 + - - +
1005B ASP* 3.5 9.7 + - + +
1013B ASN* 3.8 38.4 - - + +
1014B LYS 4.2 2.9 - - - +
1015B ARG* 3.5 49.1 - - + +
1016B PHE* 3.8 4.0 - - - -
1028B LEU* 5.8 3.2 - - + +
1030B SER* 4.2 20.2 + - - +
1031B ASP* 4.4 1.6 + - - -
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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