Contacts of the helix formed by residues 120 - 125 (chain W) in PDB entry 5XTD
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 LEU 120 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118W PRO 3.9 0.8 + - - -
119W PRO* 1.3 78.3 - - - +
121W ILE* 1.3 64.8 + - - +
122W GLY 3.1 8.3 - - - +
123W GLU* 3.2 26.3 + - + +
124W LEU* 3.4 15.0 + - - +
32h ARG* 4.6 2.7 - - - +
69h ARG* 3.1 52.2 - - + +
72h THR* 4.3 7.0 - - - +
124m TRP* 3.5 26.7 - - + -
127m TYR* 3.8 39.9 - - + -
128m GLU* 4.4 9.4 - - + +
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Residues in contact with ILE 121 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120W LEU* 1.3 73.9 - - - +
122W GLY* 1.3 58.1 + - - +
124W LEU* 3.4 5.5 + - + +
125W TYR* 3.1 47.0 + - + +
133W ALA* 4.8 4.9 - - + +
136W ALA* 4.2 27.6 - - + +
137W SER* 4.5 11.4 - - - -
124m TRP* 5.5 6.7 - - + -
126m ILE* 3.5 17.0 - - + -
127m TYR* 3.2 25.9 + - - +
128m GLU* 4.7 1.0 - - - +
129m GLY* 3.5 27.8 - - - +
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Residues in contact with GLY 122 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120W LEU* 3.1 4.9 - - - +
121W ILE* 1.3 79.5 - - - +
123W GLU* 1.3 60.1 + - - +
124W LEU 3.5 0.2 - - - -
125W TYR 4.6 2.9 - - - -
126W GLY* 3.2 25.0 - - - -
76h ALA* 4.9 7.8 - - - +
124m TRP* 3.4 46.6 - - - +
127m TYR* 6.0 0.4 - - - +
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Residues in contact with GLU 123 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87W LEU* 4.6 8.0 - - + +
90W ASN* 3.5 13.2 + - - +
119W PRO* 3.3 15.1 - - + +
120W LEU* 3.2 38.0 + - + +
121W ILE 3.2 0.6 - - - -
122W GLY* 1.3 79.6 - - - +
124W LEU* 1.3 65.0 + - - +
126W GLY* 4.2 3.5 + - - -
69h ARG* 4.1 7.8 + - - -
72h THR* 3.3 36.9 + - - +
76h ALA* 6.0 4.9 - - + -
124m TRP* 5.4 2.9 - - + -
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Residues in contact with LEU 124 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83W THR* 4.4 10.5 - - + +
86W MET* 3.6 35.9 - - + -
87W LEU* 3.6 33.4 - - + -
90W ASN* 2.8 23.1 + - - +
119W PRO* 3.6 23.3 - - + +
120W LEU 3.6 13.0 - - - +
121W ILE* 3.4 7.2 + - + +
123W GLU* 1.3 79.6 - - - +
125W TYR* 1.3 77.0 + - + +
126W GLY 3.3 3.3 + - - -
127W LEU 4.9 0.2 + - - -
128W ARG* 3.9 13.3 + - - +
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Residues in contact with TYR 125 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82W ARG* 4.0 13.9 + - - -
86W MET* 3.8 19.2 - - + +
121W ILE* 3.1 26.1 + - + +
122W GLY* 4.1 4.7 - - - -
124W LEU* 1.3 94.6 - - + +
126W GLY* 1.3 57.4 + - - +
127W LEU 3.1 7.8 + - - +
128W ARG* 3.8 30.3 + - + +
132W GLU* 3.0 47.6 - - + -
133W ALA* 4.0 27.8 - - + +
136W ALA* 3.9 24.8 - - + +
1m MET* 4.6 6.1 - - - +
124m TRP* 6.1 0.5 - - - +
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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