Contacts of the strand formed by residues 207 - 211 (chain C) in PDB entry 5M64
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 HIS 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C ALA* 3.2 7.2 - - - +
81C GLU* 3.1 23.6 + - - +
82C TYR* 3.1 14.5 + - + +
84C TYR* 3.4 29.7 - + - -
126C PHE* 3.2 39.1 - + + -
131C THR* 3.8 15.3 - - + -
132C ILE 3.4 6.3 - - - -
133C VAL* 4.8 7.1 - - + +
134C LEU* 5.6 0.2 - - - -
205C LYS* 3.0 37.2 + - - +
206C ALA* 1.3 83.7 - - - +
208C CYS* 1.3 59.8 + - - +
209C ILE* 5.6 0.2 - - - -
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Residues in contact with CYS 208 (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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78C VAL* 3.5 24.0 - - - -
79C ALA* 3.4 26.2 - - - -
80C ALA* 3.6 7.0 - - - +
106C LEU* 3.9 21.5 - - - -
108C VAL* 5.4 1.6 - - - -
130C ASN 4.1 0.7 - - - +
131C THR* 3.4 10.0 - - - +
132C ILE* 2.8 52.0 + - + +
134C LEU* 4.4 11.2 - - + +
207C HIS* 1.3 73.4 - - - +
209C ILE* 1.3 59.0 + - - +
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Residues in contact with ILE 209 (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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78C VAL* 3.4 6.8 - - - -
79C ALA 2.8 36.6 + - - +
81C GLU* 3.3 44.6 - - + +
114C THR 6.0 0.2 - - - +
116C VAL* 3.6 37.2 - - + -
125C LYS* 6.0 0.2 - - - -
126C PHE* 3.8 22.7 - - + -
130C ASN 4.3 11.0 - - - +
131C THR* 5.2 0.2 - - - +
207C HIS 4.2 0.4 + - - +
208C CYS* 1.3 74.3 - - - +
210C LEU* 1.3 81.4 - - + +
219C PHE* 3.6 5.0 - - + -
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Residues in contact with LEU 210 (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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76C PRO* 5.1 10.8 - - + -
77C SER 3.2 8.5 - - - +
78C VAL* 3.7 32.1 - - + -
110C PRO* 4.9 4.9 - - + -
111C ASP* 4.7 13.2 - - - +
113C LEU* 3.3 51.8 - - + +
114C THR 4.5 10.5 - - - +
115C TRP* 4.5 19.8 - - + -
130C ASN 4.4 6.1 - - - +
132C ILE* 6.2 0.2 - - + -
209C ILE* 1.3 99.7 - - + +
211C GLY* 1.3 59.9 + - - +
219C PHE* 3.4 5.4 - - - -
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Residues in contact with GLY 211 (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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76C PRO* 3.5 4.0 - - - +
77C SER 2.9 29.8 + - - +
115C TRP* 3.7 16.1 - - - -
210C LEU* 1.3 78.9 - - - +
212C ILE* 1.3 65.6 + - - -
219C PHE* 3.6 16.4 - - - +
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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