Contacts of the strand formed by residues 108 - 113 (chain g) in PDB entry 5OA3
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 VAL 108 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67g SER* 2.5 30.5 + - - -
81g GLY* 3.9 5.2 - - - -
82g SER 3.6 16.5 + - - +
83g TRP* 3.9 4.5 - - - -
85g GLY* 3.6 30.7 - - - +
86g THR 3.6 11.9 - - - +
87g LEU* 3.8 28.3 - - + +
104g HIS* 4.0 21.5 - - + -
107g ASP* 1.3 73.9 - - - +
109g LEU* 1.3 53.4 + - - +
110g SER 4.2 16.2 - - - +
122g SER* 4.9 5.4 - - - -
123g GLY 4.4 2.5 - - - +
124g SER* 4.2 3.1 - - - -
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Residues in contact with LEU 109 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67g SER* 3.3 19.2 + - - +
68g ASP* 4.3 3.6 - - - +
83g TRP* 4.1 14.6 - - + +
107g ASP 3.5 3.6 + - - -
108g VAL* 1.3 74.5 - - - +
110g SER* 1.3 67.4 + - - +
123g GLY 3.2 6.3 + - - +
124g SER* 4.4 3.4 - - - -
125g ARG* 3.5 55.9 - - + +
150g TRP* 4.3 10.5 - - + -
151g VAL 3.3 27.6 - - - +
152g SER* 3.7 19.9 - - - +
170g TRP* 4.6 4.7 - - + +
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Residues in contact with SER 110 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67g SER* 4.8 0.7 - - - -
68g ASP* 4.1 16.9 + - - -
108g VAL* 3.5 5.7 - - - +
109g LEU* 1.3 82.2 + - - +
111g VAL* 1.3 60.9 + - - +
122g SER* 3.3 5.1 - - - -
123g GLY 2.9 34.3 + - - +
152g SER 2.4 29.3 + - - -
153g CYS* 3.2 21.9 - - - +
154g VAL* 3.5 11.4 - - - -
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Residues in contact with VAL 111 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68g ASP* 3.9 39.6 - - + +
70g VAL* 4.3 18.2 - - + +
79g LEU* 3.5 35.9 - - + +
81g GLY* 4.1 10.8 - - - +
87g LEU* 3.6 26.0 - - + -
110g SER* 1.3 76.3 - - - +
112g ALA* 1.3 66.2 + - - +
120g ILE* 4.0 7.9 - - + -
121g VAL 3.8 2.9 - - - -
122g SER* 4.1 2.9 - - - -
154g VAL 3.9 7.0 - - - +
155g ARG* 5.3 1.7 + - - -
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Residues in contact with ALA 112 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70g VAL* 4.7 1.3 - - - -
111g VAL* 1.3 77.9 - - - +
113g PHE* 1.3 60.2 + - - +
120g ILE* 3.7 5.0 - - - +
121g VAL 2.9 43.1 + - - +
154g VAL* 3.2 32.5 - - + +
155g ARG* 3.9 7.2 - - - -
156g PHE* 3.3 20.1 - - + +
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Residues in contact with PHE 113 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70g VAL* 3.6 36.7 - - + +
71g ILE 4.1 14.4 - - - -
72g SER* 3.7 18.2 - - - -
79g LEU* 4.2 22.4 - - + -
89g LEU* 6.3 3.4 - - + -
112g ALA* 1.3 73.9 - - - +
114g SER* 1.3 69.1 + - - +
117g ASN* 3.1 54.5 - - + -
119g GLN 3.4 22.9 - - - -
120g ILE* 4.2 8.5 - - + -
134g THR* 5.7 11.2 - - + -
156g PHE* 3.5 9.7 - - - +
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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