Contacts of the strand formed by residues 116 - 120 (chain L) in PDB entry 1OZT
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 116 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L VAL* 3.2 4.3 - - - +
48L HIS* 2.7 36.1 + - - +
50L PHE 2.7 25.5 + - - -
51L GLY* 3.2 12.3 - - - -
52L ASP 4.0 2.4 + - - -
53L ASN* 6.0 0.3 - - - +
60L ALA* 3.7 15.1 - - + +
115L ARG* 1.3 74.0 + - - +
117L LEU* 1.3 71.9 + - - +
118L VAL* 3.7 9.9 - - + -
146L CYS* 3.6 19.5 - - + -
147L GLY 3.4 15.0 + - - +
148L VAL* 4.2 5.2 - - - +
149L ILE* 4.3 3.4 - - - -
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Residues in contact with LEU 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L CYS* 3.8 16.6 - - - -
8L LEU* 3.4 12.8 - - + +
18L ILE* 3.7 40.4 - - + -
20L PHE* 4.0 10.1 - - + -
45L PHE* 3.8 32.8 - - + -
46L ARG 3.4 20.6 - - - +
47L VAL* 4.2 13.0 - - + +
84L LEU* 4.5 5.4 - - + -
116L THR* 1.3 74.6 - - - +
118L VAL* 1.3 61.8 + - - +
146L CYS* 3.1 25.6 - - - +
147L GLY 3.1 6.3 + - - -
149L ILE* 4.1 10.0 - - + +
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Residues in contact with VAL 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L LEU* 4.8 0.9 - - - -
44L GLY 3.7 0.7 - - - +
45L PHE* 3.5 8.0 - - - -
46L ARG 2.6 34.6 + - - -
48L HIS* 3.2 34.8 - - + +
57L CYS* 5.1 0.4 - - + -
60L ALA* 4.6 4.7 - - + -
116L THR* 3.7 16.2 - - + -
117L LEU* 1.3 81.1 - - - +
119L VAL* 1.3 67.1 + - - +
120L HIS* 3.8 14.5 - - + +
143L ARG* 3.7 34.5 - - + -
145L ALA 3.5 11.0 - - - +
146L CYS* 3.9 6.1 - - + -
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Residues in contact with VAL 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L LEU* 4.9 5.6 - - + +
14L VAL* 3.9 21.1 - - + -
35L ILE* 4.4 19.1 - - + -
38L LEU* 4.4 11.0 - - + -
43L HIS* 3.9 20.6 - - + -
44L GLY 3.3 7.9 - - - +
45L PHE* 4.5 5.2 - - + -
87L VAL* 4.1 14.8 - - + -
118L VAL* 1.3 76.8 - - - +
120L HIS* 1.3 64.8 + - - +
144L LEU* 3.0 24.8 + - + +
145L ALA* 3.1 25.1 + - + +
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Residues in contact with HIS 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L HIS* 2.9 28.6 + - - +
44L GLY* 2.6 27.4 + - - +
46L ARG* 3.4 33.9 + - + +
48L HIS* 3.0 36.5 + + - -
118L VAL* 3.8 10.2 - - + +
119L VAL* 1.3 79.5 - - - +
121L GLU* 1.3 62.7 + - - +
122L LYS 3.3 4.0 + - - +
138L GLY 5.2 1.6 - - - -
139L ASN* 6.3 0.2 - - - -
140L ALA* 3.6 28.3 + - + +
141L GLY 4.9 1.6 + - - -
142L SER 3.5 5.5 + - - -
143L ARG* 4.1 24.1 - - + +
144L LEU* 3.8 4.5 - - - +
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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