Contacts of the strand formed by residues 549 - 554 (chain C) in PDB entry 2FH2
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 THR 549 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509C MET* 3.4 10.1 - - - +
514C GLY 6.1 0.7 - - - -
516C PRO* 3.4 20.8 - - + +
517C MET 3.1 21.8 + - - -
541C VAL* 3.6 29.2 - - + -
542C ARG 3.7 6.7 - - - +
543C ALA* 3.3 14.2 - - + +
547C GLY 3.1 14.5 + - - -
548C ALA* 1.3 70.3 - - - +
550C ARG* 1.3 65.0 + - - +
586C ALA* 3.6 23.1 + - - +
587C GLU* 4.6 0.4 - - - -
590C GLY* 4.3 2.9 - - - -
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Residues in contact with ARG 550 (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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502C GLY* 3.6 12.8 + - - +
504C GLU* 2.9 49.9 + - - -
509C MET* 3.6 26.9 - - + +
516C PRO* 4.8 0.9 - - - -
517C MET* 3.4 14.6 - - + +
519C ILE* 5.6 2.9 - - + -
540C GLN 3.8 0.4 - - - +
541C VAL* 3.2 7.8 - - - +
542C ARG 2.9 36.5 + - - +
544C ASN* 4.0 16.4 - - - +
548C ALA 4.1 8.1 + - - -
549C THR* 1.3 77.0 - - - +
551C ALA* 1.3 59.9 + - - +
552C VAL* 4.0 15.3 - - + -
659C GLY* 6.0 0.8 - - - -
660C GLU* 3.6 42.3 + - - +
662C MET* 5.9 0.2 - - - -
734C LEU* 4.0 13.0 - - + -
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Residues in contact with ALA 551 (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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516C PRO* 5.1 5.2 - - + -
517C MET 2.8 12.4 + - - +
518C ILE* 3.5 18.1 - - + +
519C ILE 3.0 25.3 + - - +
539C PHE* 4.1 4.1 - - - -
540C GLN 3.4 5.2 - - - -
541C VAL* 4.0 15.5 - - + +
550C ARG* 1.3 74.5 - - - +
552C VAL* 1.3 60.3 + - - +
590C GLY 5.3 0.2 - - - +
594C LEU* 4.0 28.7 - - + -
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Residues in contact with VAL 552 (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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501C GLN* 4.2 20.0 - - - +
519C ILE* 3.9 19.7 - - + +
539C PHE* 3.9 2.7 - - - -
540C GLN* 2.8 38.8 + - + +
550C ARG* 4.2 13.0 - - + -
551C ALA* 1.3 76.7 - - - +
553C GLU* 1.3 74.9 + - - +
554C VAL* 3.5 6.7 + - + +
662C MET* 5.4 1.6 - - + -
734C LEU* 4.0 42.4 - - + +
735C GLY* 5.8 1.1 - - - -
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Residues in contact with GLU 553 (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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519C ILE 3.0 17.4 + - - +
520C TYR* 3.7 0.7 - - - -
521C LYS* 2.8 57.2 + - + +
534C ALA* 5.3 4.7 + - - +
536C THR 5.3 0.2 - - - +
537C ARG* 2.7 55.3 + - - +
538C LEU 3.2 17.0 - - - +
539C PHE* 3.5 21.5 - - + -
552C VAL* 1.3 79.7 - - - +
554C VAL* 1.3 68.7 + - - +
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Residues in contact with VAL 554 (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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521C LYS* 3.9 13.5 - - - +
537C ARG* 5.5 0.2 - - - -
538C LEU* 3.0 43.8 + - + +
540C GLN* 4.5 11.4 - - + +
552C VAL* 4.0 11.4 - - + +
553C GLU* 1.3 84.2 - - - +
555C LEU* 1.3 75.2 + - - +
556C PRO* 3.5 5.0 - - - +
560C ALA* 4.1 13.9 - - + +
567C PHE* 4.5 10.1 - - + -
735C GLY* 4.2 25.6 - - - -
736C TRP 5.4 0.4 - - - +
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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