Contacts of the strand formed by residues 1023 - 1032 (chain C) in PDB entry 5UHF
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 VAL1023 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722C ALA* 4.6 1.1 - - + -
723C ILE 4.0 5.6 - - - +
724C MET* 3.9 36.6 - - + -
1007C LYS* 3.7 0.9 - - - -
1008C ALA 2.6 40.0 + - - +
1010C LEU* 3.7 43.1 - - + +
1019C PHE* 4.5 9.4 - - + -
1021C TYR 3.5 14.4 - - - +
1022C PRO* 1.3 72.5 - - - +
1024C THR* 1.3 72.4 + - - +
1025C VAL* 3.2 6.1 - - + +
728D GLY* 6.6 0.2 - - - -
730D THR* 4.5 4.9 - - - +
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Residues in contact with THR1024 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722C ALA* 3.6 2.8 - - - -
723C ILE* 3.0 41.5 + - + +
931C ILE* 5.4 2.7 - - + -
934C THR* 4.4 10.8 - - + -
935C HIS* 4.1 18.2 - - + -
1006C GLY 3.9 9.6 - - - +
1007C LYS* 3.3 21.8 - - - +
1023C VAL* 1.3 72.7 - - - +
1025C VAL* 1.3 61.2 + - - +
730D THR* 3.2 26.7 - - - +
731D VAL 3.5 12.4 + - - +
732D SER* 3.5 12.7 - - - -
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Residues in contact with VAL1025 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720C LEU* 4.2 12.3 - - + -
721C VAL 3.4 15.3 - - - +
722C ALA* 4.8 2.0 - - + -
907C LEU* 4.2 23.6 - - + -
913C VAL* 4.6 5.8 - - + -
934C THR* 3.7 11.1 - - - +
935C HIS* 5.2 1.2 + - - -
938C TRP* 4.3 8.3 - - + +
1002C VAL* 4.5 9.5 - - + +
1006C GLY 3.4 16.3 + - - +
1008C ALA* 4.2 15.7 - - + -
1010C LEU* 4.2 28.5 - - + -
1023C VAL* 3.2 19.1 + - + +
1024C THR* 1.3 76.7 - - - +
1026C GLY* 1.3 64.3 + - - +
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Residues in contact with GLY1026 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720C LEU* 3.5 10.1 - - - +
721C VAL* 2.8 34.3 + - - +
934C THR* 3.5 13.5 - - - -
938C TRP* 3.8 15.3 - - - -
1025C VAL* 1.3 82.4 - - - +
1027C TYR* 1.3 65.8 + - - -
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Residues in contact with TYR1027 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C LEU* 4.4 13.9 - - + -
626C VAL* 5.4 0.5 - - - +
718C ASN* 4.0 26.5 - - + -
719C LEU 3.3 24.7 - - - -
720C LEU* 3.6 30.2 - - + +
914C ASP* 5.0 2.0 - - - -
933C GLU* 2.9 24.9 - - - +
934C THR* 3.4 10.8 + - - +
937C GLY* 3.6 18.5 - - - +
938C TRP* 3.9 11.7 - + - +
941C HIS* 3.3 56.7 + + + -
1026C GLY* 1.3 76.4 - - - -
1028C MET* 1.3 61.4 + - - +
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Residues in contact with MET1028 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717C LYS 3.6 0.2 - - - +
718C ASN* 4.5 3.4 - - - -
719C LEU* 2.8 34.5 + - + +
721C VAL* 3.8 16.6 - - + +
723C ILE* 4.7 5.4 - - + -
887C GLY* 5.3 2.2 - - - -
889C HIS* 5.4 0.9 - - + -
891C ASN* 4.1 16.8 - - - -
915C ILE* 6.2 0.2 - - + -
917C LEU* 3.8 30.7 - - + -
930C GLN* 3.5 23.6 - - + +
933C GLU* 3.3 22.7 - - + +
934C THR* 3.3 20.0 - - - +
1026C GLY 4.3 0.4 - - - -
1027C TYR* 1.3 73.9 - - - +
1029C TYR* 1.3 69.1 + - - +
1030C ILE* 3.7 17.4 + - + +
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Residues in contact with TYR1029 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622C GLU 2.8 20.3 + - - -
624C PRO* 3.5 44.1 - - + +
626C VAL 6.2 0.2 - - - +
713C MET 5.0 0.4 - - - -
714C ALA* 3.1 3.3 - - - -
715C LEU* 3.0 22.2 + - + -
716C GLY* 2.7 48.1 + - - -
717C LYS 3.2 16.6 - - - -
718C ASN* 3.6 8.9 + - - +
887C GLY* 4.0 12.6 - - - -
888C ARG* 3.4 35.8 + - + +
933C GLU* 2.6 21.2 + - - +
1028C MET* 1.3 71.3 - - - +
1030C ILE* 1.3 67.4 + - - +
1031C MET* 4.3 4.3 + - + +
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Residues in contact with ILE1030 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716C GLY* 3.2 2.2 - - - -
717C LYS* 2.8 37.7 + - - +
719C LEU* 3.9 29.6 - - + -
721C VAL* 6.5 0.2 - - + -
747C LEU* 4.7 5.8 - - + +
885C LEU* 3.8 35.2 - - + -
886C ALA 3.9 3.6 - - - +
887C GLY* 4.4 11.9 - - - +
891C ASN* 5.7 0.7 - - - +
915C ILE* 4.5 19.1 - - + -
917C LEU* 5.8 1.8 - - + -
1028C MET* 3.9 31.4 - - + +
1029C TYR* 1.3 84.5 - - - +
1031C MET* 1.3 70.7 + - - +
1032C LYS 4.2 0.5 + - - -
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Residues in contact with MET1031 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608C GLY 5.1 0.2 - - - +
611C MET* 4.6 2.0 - - + -
612C GLN* 3.7 44.9 - - + +
615C ALA* 4.3 9.6 - - + -
715C LEU* 3.2 39.3 - - + +
716C GLY* 4.2 0.9 - - - +
747C LEU* 5.1 0.2 - - - -
885C LEU* 3.3 9.4 - - - +
886C ALA* 2.9 53.9 + - + +
887C GLY 3.7 20.9 - - - +
888C ARG* 4.2 9.9 - - + +
1029C TYR* 4.8 8.3 - - + +
1030C ILE* 1.3 75.3 - - - +
1032C LYS* 1.3 61.8 + - - +
1033C LEU* 3.6 9.6 + - + +
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Residues in contact with LYS1032 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C ALA* 4.5 0.4 - - - -
616C VAL* 2.9 33.1 + - + +
618C LEU* 4.2 19.4 - - + +
715C LEU 4.4 3.8 + - - -
716C GLY* 5.1 1.2 - - - -
747C LEU* 3.5 31.0 + - + +
749C SER* 2.6 35.0 + - - +
751C HIS* 4.3 1.4 + - - -
877C ARG* 3.4 20.2 + - - +
879C ILE* 4.8 16.4 - - + +
883C ASP* 5.0 3.6 + - + -
884C LYS 5.2 0.7 - - - +
885C LEU* 3.6 17.5 - - + -
1030C ILE 4.2 0.8 + - - -
1031C MET* 1.3 70.2 - - - +
1033C LEU* 1.3 70.1 + - - +
1036C LEU* 3.8 28.9 - - + +
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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