Contacts of the helix formed by residues 110 - 119 (chain F) in PDB entry 5ZX2
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 110 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1062C GLN* 6.2 0.4 - - - +
108F GLN* 3.5 6.2 + - - -
109F ILE* 1.3 78.4 - - - +
111F ASP* 1.3 68.3 + - + +
112F TRP* 3.3 24.0 - - + +
113F GLN* 3.0 36.5 + - - +
114F LEU* 3.1 10.7 + - - +
19H G 4.5 5.0 + - - +
1I C 3.2 32.0 + - - +
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Residues in contact with ASP 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050C SER* 4.6 5.5 + - - -
1056C PRO 4.9 0.9 - - - +
1057C LEU* 3.6 35.4 - - + +
1058C GLY* 3.2 35.2 + - - +
1062C GLN* 3.8 5.5 - - + +
421D ARG* 5.1 5.2 + - - -
108F GLN* 5.9 0.2 + - - -
109F ILE 4.5 3.3 - - - +
110F THR* 1.3 76.8 - - + +
112F TRP* 1.3 61.9 + - - +
114F LEU* 3.3 10.8 + - - +
115F ALA* 3.0 24.9 + - - +
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Residues in contact with TRP 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C ALA* 5.6 3.1 - - + -
1062C GLN* 3.3 32.9 - - + +
330D LEU* 5.7 3.4 - - + -
331D ASP* 4.2 24.9 - - + -
110F THR* 3.2 15.7 - - + +
111F ASP* 1.3 78.6 - - - +
113F GLN* 1.3 78.3 + - + +
115F ALA* 5.9 1.3 - - + -
116F SER* 2.9 44.9 + - - -
19H G 5.7 10.3 - + - -
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Residues in contact with GLN 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D VAL* 4.5 4.9 - - + +
329D GLN 4.8 2.6 - - - +
330D LEU* 3.8 39.7 - - + +
336D ALA* 4.5 10.3 - - - +
106F THR* 4.9 4.5 + - - -
108F GLN 4.4 1.9 - - - +
109F ILE* 3.5 19.6 - - + +
110F THR* 3.0 40.0 + - - +
112F TRP* 1.3 96.5 - - + +
114F LEU* 1.3 56.1 + - - +
116F SER* 3.8 4.0 - - - -
117F ASN* 2.9 30.5 + - - +
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049C TYR 5.4 0.2 - - - +
1050C SER* 3.7 36.8 - - - +
1051C MET* 4.0 25.6 - - + +
1052C ILE* 4.2 13.2 - - + -
1057C LEU* 4.3 10.5 - - + -
328D VAL* 3.8 25.6 - - + -
109F ILE* 3.8 13.5 - - + +
110F THR 3.1 15.4 + - - +
111F ASP* 3.3 11.6 + - - +
113F GLN* 1.3 76.8 - - - +
115F ALA* 1.3 58.0 + - - +
117F ASN* 3.3 6.4 + - + +
118F ALA* 2.9 27.7 + - - +
125F LEU* 4.2 9.2 - - + +
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048C PRO* 6.0 0.7 - - + -
1057C LEU* 4.2 10.3 - - + -
1062C GLN* 4.1 19.7 - - + +
111F ASP 3.0 15.6 + - - +
112F TRP* 4.1 3.4 - - + +
114F LEU* 1.3 75.8 - - - +
116F SER* 1.3 65.3 + - - +
118F ALA* 2.9 12.7 + - - +
119F GLU* 3.0 22.8 + - + +
125F LEU* 3.9 13.8 - - + +
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Residues in contact with SER 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760C ARG* 5.5 0.2 + - - -
329D GLN 5.2 2.4 + - - -
330D LEU* 5.5 2.1 - - - +
331D ASP* 3.2 29.0 + - - -
112F TRP* 2.9 40.6 + - - -
113F GLN* 3.8 6.2 + - - -
115F ALA* 1.3 75.8 - - - +
117F ASN* 1.3 62.7 + - - +
119F GLU* 3.5 12.4 + - - +
120F HIS* 3.4 21.7 + - - -
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Residues in contact with ASN 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760C ARG* 5.4 3.5 + - - +
1051C MET* 6.3 1.0 - - - +
328D VAL* 4.2 16.5 - - + +
329D GLN* 3.2 46.0 + - - +
113F GLN 2.9 19.1 + - - +
114F LEU* 3.6 6.0 + - - +
115F ALA 3.2 0.2 - - - -
116F SER* 1.3 77.4 + - - +
118F ALA* 1.3 63.4 + - - +
119F GLU 3.4 0.5 + - - -
120F HIS* 3.4 16.1 + - - +
121F SER* 3.6 12.0 + - - -
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833C ARG* 3.1 19.9 + - - -
114F LEU 2.9 15.9 + - - +
115F ALA 2.9 5.1 + - - +
117F ASN* 1.3 73.8 - - - +
119F GLU* 1.3 67.7 + - - +
120F HIS 3.1 2.5 - - - -
121F SER* 3.1 16.4 + - - -
123F THR 5.2 0.2 - - - +
124F GLY* 4.0 3.2 - - - -
125F LEU* 3.5 39.5 - - + +
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Residues in contact with GLU 119 (chain F).
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* 5.4 7.6 - - + -
805C LYS* 3.8 5.7 + - - +
833C ARG* 4.6 2.3 + - - +
835C THR* 3.2 47.1 - - - +
836C SER 4.9 3.3 - - - +
837C LEU* 6.0 0.3 - - - -
115F ALA* 3.0 22.5 + - - +
116F SER* 3.7 13.5 - - - +
117F ASN 3.2 1.0 - - - -
118F ALA* 1.3 78.6 - - - +
120F HIS* 1.3 67.0 + - + +
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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