Contacts of the helix formed by residues 113 - 120 (chain I) in PDB entry 1ZUM
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 PRO 113 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111I GLY 3.7 1.3 - - - +
112I LYS* 1.3 88.3 - - + +
114I TYR* 1.3 66.3 + - - +
115I VAL* 4.4 4.3 - - + +
116I ILE* 3.0 29.4 + - + +
117I SER* 3.0 19.2 + - - -
297I ASN* 5.9 2.0 - - - -
298I GLN* 3.5 15.0 - - - +
334I PRO* 3.5 14.8 - - + +
336I ASP 5.8 0.2 - - - +
339I THR* 4.1 17.3 - - + +
340I GLU* 3.6 30.3 - - - +
341I GLN 4.3 0.2 - - - +
342I GLY* 4.2 6.3 - - - +
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 4.3 14.8 - - + -
9I PRO 2.8 28.8 + - - -
11I PRO* 3.5 35.4 - - + +
100I THR* 3.4 24.4 - - - +
103I ALA* 3.7 22.0 - - + -
104I ALA* 3.7 23.6 - - - -
107I THR* 3.1 16.5 + - - +
112I LYS 3.4 0.4 + - - -
113I PRO* 1.3 70.1 - - - +
115I VAL* 1.3 72.5 + - + +
117I SER* 3.3 2.0 + - - -
118I TYR* 3.0 36.8 + + + +
334I PRO 3.0 13.7 + - - +
335I PHE* 3.8 22.0 - + + -
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Residues in contact with VAL 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 4.1 25.8 - - + -
113I PRO* 3.2 4.1 - - + +
114I TYR* 1.3 83.4 - - + +
116I ILE* 1.3 66.7 + - + +
118I TYR* 3.9 3.5 - - - +
119I LEU* 3.0 50.6 + - + +
334I PRO 4.9 0.6 + - - -
336I ASP 5.6 0.7 - - - +
337I SER* 4.5 30.3 - - - +
339I THR 6.0 1.1 - - - +
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Residues in contact with ILE 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I LYS* 5.1 6.1 - - + -
113I PRO* 3.0 34.2 + - + +
115I VAL* 1.3 85.7 - - + +
117I SER* 1.3 59.0 + - - +
119I LEU* 6.2 0.2 - - + -
120I VAL* 2.7 62.0 + - + +
121I ASP* 3.2 10.8 + - - +
296I PHE* 3.9 23.6 - - + -
297I ASN* 6.1 1.6 - - + +
340I GLU* 5.5 2.5 - - - +
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Residues in contact with SER 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I ALA* 3.4 26.5 + - - -
106I GLU* 3.9 9.1 - - - +
107I THR* 2.9 19.2 + - - -
112I LYS* 3.1 21.3 - - - +
113I PRO 3.0 5.1 + - - -
114I TYR 3.4 8.5 - - - -
116I ILE* 1.3 78.0 - - - +
118I TYR* 1.3 56.6 + - - -
121I ASP* 3.4 12.0 - - - +
122I LEU* 2.9 35.8 + - - +
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Residues in contact with TYR 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ALA 4.7 3.1 - - - -
8I VAL* 4.2 10.5 - - + -
9I PRO* 3.5 33.2 - - + +
99I ARG* 2.7 83.8 + - + +
100I THR* 3.9 16.1 + - - -
103I ALA* 3.7 14.4 - - + -
114I TYR* 3.0 37.1 + - + +
115I VAL* 3.9 4.9 - - - +
117I SER* 1.3 79.4 - - - +
119I LEU* 1.3 73.1 + - + +
122I LEU* 3.6 6.0 - - - +
123I ASP 3.9 0.3 + - - -
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Residues in contact with LEU 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ALA 4.9 11.4 - - - +
8I VAL* 3.7 25.6 - - + -
99I ARG* 4.0 6.5 + - - +
115I VAL* 3.0 30.7 + - + +
116I ILE* 6.2 0.4 - - + -
118I TYR* 1.3 93.1 - - + +
120I VAL* 1.3 65.4 + - + +
123I ASP* 3.3 19.7 - - - +
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Residues in contact with VAL 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I ILE* 2.7 46.4 + - + +
119I LEU* 1.3 79.9 - - + +
121I ASP* 1.3 62.0 + - - +
122I LEU 3.5 0.2 - - - -
123I ASP* 3.2 2.8 + - - +
124I MET* 2.9 60.3 + - + +
296I PHE* 4.2 21.3 - - + -
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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