Contacts of the strand formed by residues 119 - 124 (chain A) in PDB entry 2O05
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 SER 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ARG 3.2 3.4 + - - +
96A LYS* 3.5 20.9 - - - -
97A VAL 2.9 25.2 + - - -
117A VAL* 3.7 1.8 - - - +
118A GLU* 1.3 81.0 - - - +
120A VAL* 1.3 69.4 + - - +
121A VAL* 4.1 11.5 - - - +
148A LYS 3.6 7.5 + - - -
150A THR* 4.6 6.6 + - - -
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Residues in contact with VAL 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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97A VAL* 3.3 13.5 - - + +
99A ILE* 3.5 38.1 - - + -
108A LEU* 3.6 14.1 - - + -
111A VAL* 3.5 13.2 - - + -
112A VAL* 4.0 16.6 - - + -
117A VAL* 3.4 28.7 - - + -
119A SER* 1.3 71.4 - - - +
121A VAL* 1.3 62.2 - - - +
122A GLN 4.9 0.4 - - - +
148A LYS* 3.0 11.8 + - + +
149A LEU* 3.3 5.7 - - - +
150A THR 2.7 31.0 + - - +
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Residues in contact with VAL 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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97A VAL 2.9 5.9 + - - -
98A LEU* 3.3 8.7 - - + +
99A ILE 2.8 25.5 + - - -
119A SER* 4.4 9.4 - - - +
120A VAL* 1.3 75.1 - - - +
122A GLN* 1.3 62.4 + - - +
150A THR* 3.4 29.6 - - + +
152A HIS* 4.4 13.5 - - + -
159A PHE* 3.8 28.9 - - + -
167A PHE* 3.9 27.1 - - + -
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Residues in contact with GLN 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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99A ILE* 3.3 25.9 - - + +
101A GLY 3.4 22.0 - - - +
102A GLY* 3.1 16.3 + - - +
103A GLY* 4.1 1.4 - - - -
108A LEU* 3.8 27.9 - - - +
120A VAL 3.9 1.2 + - - -
121A VAL* 1.3 74.1 - - - +
123A CYS* 1.3 56.4 + - - +
124A GLU* 4.3 2.9 - - - +
144A TYR* 2.8 34.7 + - - -
149A LEU* 3.9 17.0 - - + -
150A THR 3.0 7.9 + - - -
151A LEU* 3.5 10.7 - - + +
152A HIS* 2.5 37.4 + - - +
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Residues in contact with CYS 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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98A LEU* 4.4 0.6 - - + +
99A ILE 2.9 8.9 + - - -
100A ILE* 3.6 20.4 - - + -
101A GLY 2.8 30.3 + - - -
121A VAL 4.1 1.0 + - - -
122A GLN* 1.3 71.5 - - - +
124A GLU* 1.3 53.0 + - - +
152A HIS* 3.6 12.8 - - + -
153A VAL 4.3 1.1 - - - -
154A GLY* 3.6 28.9 - - - -
156A GLY* 4.2 4.5 - - - -
159A PHE* 3.6 44.0 - - + -
501A MTA 3.4 7.7 - - - -
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Residues in contact with GLU 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 GLY 3.5 11.1 - - - +
103A GLY* 3.2 15.3 + - - -
122A GLN* 3.8 8.2 + - + +
123A CYS* 1.3 74.8 - - - +
125A ILE* 1.3 64.8 + - - +
126A ASP* 2.7 38.2 + - - +
127A GLU* 5.1 0.9 + - - +
130A ILE* 3.7 30.2 - - + +
151A LEU* 4.8 0.9 - - + -
152A HIS 3.2 8.3 + - - +
153A VAL* 3.6 10.4 - - - +
154A GLY 3.2 16.1 + - - -
501A MTA 2.7 53.2 + - - -
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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