Contacts of the strand formed by residues 119 - 124 (chain A) in PDB entry 1G83
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 TRP 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.2 29.8 - + - -
96A ARG* 5.5 7.6 - - + -
100A ASP* 3.8 13.2 - - - -
116A GLU* 3.9 22.1 - - + +
117A GLY 3.3 2.6 + - - -
118A ASP* 1.3 94.3 - - + +
120A TRP* 1.3 72.2 + - - +
132A TYR* 4.0 19.5 - - + -
133A ILE* 3.4 10.5 - - - -
134A PRO* 3.5 37.9 - - + -
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Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PHE* 3.9 34.8 - + - -
111A ILE* 3.9 25.6 - - + -
113A ASN 3.4 5.6 - - - +
114A SER* 3.4 38.9 + - - +
117A GLY 3.4 19.7 + - - -
119A TRP* 1.3 88.4 - - - +
121A GLU* 1.3 65.0 + - - +
132A TYR* 3.2 6.6 - - - -
133A ILE* 2.8 51.2 + - + +
135A SER* 3.5 30.0 - - - -
138A VAL* 4.5 9.0 - - + -
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 4.5 4.1 - - - +
111A ILE* 3.8 3.8 - - - +
112A LEU* 2.9 45.4 + - + +
113A ASN* 2.9 29.5 + - + +
120A TRP* 1.3 71.2 - - - +
122A ALA* 1.3 62.0 + - - +
130A THR* 3.9 15.5 - - - +
131A GLY* 3.7 17.0 - - - -
132A TYR* 3.5 38.6 + - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.5 2.6 - - + +
109A PHE* 4.3 12.1 - - + -
110A GLN 3.4 12.3 - - - +
111A ILE* 4.3 8.7 - - + -
112A LEU* 4.3 6.3 - - - +
121A GLU* 1.3 77.5 - - - +
123A ARG* 1.3 60.8 + - - +
124A SER 4.2 0.7 - - - -
129A GLU 4.0 0.5 - - - +
130A THR* 3.3 5.9 + - - +
131A GLY 2.8 37.1 + - - +
133A ILE* 3.9 30.1 - - + -
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.5 2.9 - - - -
110A GLN* 3.0 65.8 + - + +
112A LEU* 4.5 7.6 - - + -
122A ALA* 1.3 75.0 - - - +
124A SER* 1.3 69.8 + - - +
125A LEU* 3.4 9.0 + - + +
128A GLY* 3.4 34.0 + - - +
129A GLU 3.4 4.3 - - - +
130A THR* 3.9 11.6 + - - +
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.0 21.1 - - - +
107A GLU* 2.4 31.2 + - - -
108A LYS 3.7 7.9 - - - -
109A PHE* 3.8 9.7 - - - -
123A ARG* 1.3 73.3 + - - +
125A LEU* 1.3 60.0 + - - +
126A THR 3.1 5.9 + - - -
127A THR* 3.4 19.4 + - - -
128A GLY* 2.9 28.2 + - - -
129A GLU 3.0 7.7 + - - -
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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