Contacts of the strand formed by residues 749 - 760 (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 SER 749 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616C VAL* 3.7 10.5 - - - -
617C PRO 3.3 21.5 - - - -
618C LEU* 4.2 1.8 - - - +
619C VAL* 4.5 1.6 - - - +
748C THR* 1.3 77.8 - - - +
750C ILE* 1.3 65.9 + - - +
751C HIS* 2.5 31.6 + - - -
876C LYS* 3.7 4.9 - - - +
877C ARG 3.1 27.2 + - - -
1032C LYS* 2.6 26.4 + - - +
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Residues in contact with ILE 750 (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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63A PHE* 4.0 26.7 - - + -
74A THR* 5.2 6.5 - - + -
616C VAL* 5.3 0.2 - - - +
617C PRO 4.1 6.1 + - - +
618C LEU 5.4 2.5 - - - +
619C VAL* 4.8 27.4 - - + +
675C PHE* 4.1 23.6 - - + -
682C THR* 4.1 0.7 - - - +
683C CYS* 3.6 46.6 + - + +
685C ASN* 5.6 3.1 - - + +
749C SER* 1.3 79.2 - - - +
751C HIS* 1.3 79.8 + - - +
752C ILE* 5.0 1.3 - - + -
874C ALA* 4.8 6.7 - - + -
875C GLN 3.4 11.0 - - - +
876C LYS* 5.3 4.7 - - + -
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Residues in contact with HIS 751 (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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616C VAL* 3.7 22.0 - - + -
681C GLY 3.3 17.8 + - - +
682C THR* 4.5 6.3 - - + +
749C SER* 2.5 30.4 + - - -
750C ILE* 1.3 79.1 + - - +
752C ILE* 1.3 64.9 + - - +
753C GLU* 6.4 0.9 - - + -
874C ALA* 3.4 1.4 - - - -
875C GLN* 2.7 44.5 + - + +
877C ARG* 3.4 47.7 + - + +
1034C HIS* 4.5 11.9 + + - -
1036C LEU* 3.7 22.9 - - + +
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Residues in contact with ILE 752 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C PHE* 3.5 28.7 - - + +
676C ALA 3.9 4.0 - - - +
677C ARG* 2.8 58.7 + - + +
681C GLY* 3.1 19.3 + - - +
682C THR 4.8 3.1 - - - +
683C CYS* 4.3 17.3 - - - -
750C ILE* 5.0 1.3 - - + -
751C HIS* 1.3 78.4 - - - +
753C GLU* 1.3 68.5 + - - +
848C ILE* 4.1 24.5 - - + -
872C TYR* 4.4 10.5 - - + -
873C VAL 3.5 11.4 - - - +
874C ALA* 4.6 5.4 - - + -
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Residues in contact with GLU 753 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ARG* 3.5 18.1 + - - +
681C GLY* 5.9 0.9 - - - -
751C HIS* 4.3 0.9 + - + -
752C ILE* 1.3 79.0 - - - +
754C GLU* 1.3 67.7 + - - +
755C HIS* 3.6 24.2 + - - +
843C GLU* 3.4 32.2 - - - +
871C VAL 3.8 0.7 - - - +
872C TYR* 3.6 6.6 - - - +
873C VAL* 3.0 33.2 + - + +
875C GLN* 4.3 11.4 - - - +
877C ARG* 5.5 4.2 + - - +
1039C ASP* 5.5 2.4 - - - +
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Residues in contact with GLU 754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ARG* 3.4 27.7 + - - +
753C GLU* 1.3 78.5 + - - +
755C HIS* 1.3 72.2 + - - +
756C GLU* 4.1 11.5 + - + +
870C ARG* 4.1 24.7 + - + -
871C VAL 4.1 2.2 - - - +
872C TYR* 3.2 37.7 + - + -
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Residues in contact with HIS 755 (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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753C GLU* 3.6 27.2 - - + +
754C GLU* 1.3 75.3 + - - +
756C GLU* 1.3 61.2 + - - +
802C LEU* 4.1 29.4 - - + -
837C LEU* 4.1 13.0 - - + +
839C VAL* 5.4 1.4 - - + +
840C PRO* 3.7 33.3 - - + +
843C GLU* 3.9 26.6 - - - +
869C VAL 4.1 0.3 - - - +
870C ARG* 3.6 4.3 - - - +
871C VAL* 3.1 42.6 + - + +
873C VAL* 4.3 17.6 - - + +
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Residues in contact with GLU 756 (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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754C GLU* 4.1 12.2 + - - +
755C HIS* 1.3 76.4 - - - +
757C ILE* 1.3 66.8 + - - +
837C LEU* 3.9 10.2 - - - +
868C LEU* 3.8 22.5 - - + +
869C VAL 3.6 2.9 - - - +
870C ARG* 2.4 56.4 + - + +
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Residues in contact with ILE 757 (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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756C GLU* 1.3 76.0 - - - +
758C ASP* 1.3 79.1 + - - +
760C ARG* 6.0 0.7 - - - +
769C ILE* 5.1 3.1 - - + -
803C VAL* 3.7 37.2 - - + -
805C LYS* 3.8 21.1 - - + +
835C THR 3.7 22.4 - - - +
836C SER 4.3 0.7 - - - -
837C LEU* 3.6 33.4 - - + +
867C GLU 4.4 0.2 - - - +
868C LEU* 3.2 5.5 - - - +
869C VAL* 3.0 32.5 + - + +
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Residues in contact with ASP 758 (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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757C ILE* 1.3 81.7 - - - +
759C ALA* 1.3 60.8 + - - +
760C ARG* 3.7 36.2 + - - +
767C GLU* 3.1 11.8 - - - +
769C ILE* 5.0 2.5 - - - -
805C LYS* 3.2 18.5 + - - +
865C VAL* 3.8 25.1 - - + +
867C GLU 3.5 6.5 - - - -
868C LEU* 3.9 13.5 - - + -
331D ASP* 4.5 4.2 - - - +
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Residues in contact with ALA 759 (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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758C ASP* 1.3 74.7 - - - +
760C ARG* 1.3 61.7 + - - +
767C GLU* 3.2 31.9 - - + +
768C GLU* 5.0 0.4 - - - -
769C ILE* 4.3 15.9 - - + +
805C LYS* 4.7 0.4 - - + -
865C VAL* 3.2 6.6 - - - -
866C ASN* 2.9 31.2 + - + -
867C GLU* 3.0 26.0 + - + +
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Residues in contact with ARG 760 (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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757C ILE* 6.0 0.4 - - - +
758C ASP* 3.7 30.2 + - - +
759C ALA* 1.3 78.2 - - - +
761C ASP* 1.3 70.4 + - - +
762C THR 3.9 0.4 - - - -
766C ALA* 3.4 2.9 - - - +
767C GLU* 2.9 69.3 + - + +
805C LYS* 4.5 8.5 - - - +
835C THR* 6.2 0.2 - - - +
864C GLY 3.3 10.3 - - - +
865C VAL* 5.0 5.6 - - + -
866C ASN* 4.2 1.1 + - - -
331D ASP* 2.9 62.1 + - - +
332D GLY 5.9 0.2 - - - -
333D GLY* 5.7 1.8 - - - +
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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