Contacts of the strand formed by residues 111 - 114 (chain S) in PDB entry 2X86
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 PHE 111 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S ILE* 3.7 8.7 - - + -
74S HIS* 3.7 37.7 - + + -
97S SER 4.1 13.5 - - - -
100S LEU* 3.7 20.6 - - + -
101S LEU* 3.8 25.8 - - + -
104S CYS* 3.8 25.6 - - + -
105S LEU* 6.3 0.2 - - + -
109S ILE 4.0 7.0 - - - +
110S PRO* 1.3 73.1 - - - +
112S LEU* 1.3 64.5 + - - +
113S TYR* 3.5 30.5 - + + -
147S PHE* 4.0 15.5 - + - -
161S GLN 3.0 12.3 + - - +
162S ILE* 3.3 8.6 - - + -
163S VAL 2.9 24.1 + - - +
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Residues in contact with LEU 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S ALA* 4.3 11.7 - - + -
72S ILE 2.9 14.3 + - - +
73S PHE* 3.2 26.1 - - + -
74S HIS* 2.7 30.6 + - - -
75S GLU* 3.7 4.4 - - - +
110S PRO* 4.0 17.7 - - + +
111S PHE* 1.3 79.8 - - - +
113S TYR* 1.3 54.9 + - - +
161S GLN* 4.0 16.6 - - - +
163S VAL* 3.3 13.9 - - + +
165S PHE* 4.2 13.7 - - + -
221S ASN* 4.1 8.5 - - - +
224S PHE* 4.0 15.0 - - + -
225S LEU* 3.9 27.8 - - + +
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Residues in contact with TYR 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S HIS* 3.5 17.5 - + + +
75S GLU* 4.5 4.5 - - - -
97S SER* 5.9 0.2 - - - -
111S PHE* 3.5 36.6 - + + -
112S LEU* 1.3 74.8 - - - +
114S ALA* 1.3 78.3 + - - +
115S SER* 4.1 1.6 - - - -
147S PHE* 3.7 16.8 - + - -
148S ASP* 2.7 29.7 + - - -
151S VAL* 3.5 33.4 - - + +
162S ILE* 4.2 7.0 - - + -
163S VAL 2.7 27.9 + - - +
164S GLY* 3.4 22.9 - - - -
165S PHE* 2.9 31.5 + - - -
232S ILE* 3.7 15.9 - - - +
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Residues in contact with ALA 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S HIS 3.2 11.3 + - - +
75S GLU* 3.7 8.5 - - - +
113S TYR* 1.3 83.9 - - - +
115S SER* 1.3 59.6 + - - +
144S LYS* 3.0 21.0 + - - +
147S PHE* 5.8 0.2 - - - -
165S PHE 3.9 3.6 - - - -
167S TYR* 3.5 26.7 - - + -
400S NAP 3.4 30.1 - - - +
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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