Contacts of the strand formed by residues 143 - 147 (chain C) in PDB entry 2W8B
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 ILE 143 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 5.3 0.2 - - + -
102C LYS* 3.4 4.7 - - - +
103C VAL* 3.5 14.4 - - + -
105C VAL* 3.9 27.1 - - + -
130C LYS* 2.6 60.8 + - + +
133C LEU* 4.1 23.8 - - + -
134C GLN* 4.1 20.6 - - + +
138C VAL* 4.3 7.9 - - + -
139C SER 4.1 8.5 - - - +
140C ALA 3.3 3.9 + - - +
141C ASP 3.4 2.0 + - - -
142C GLN* 1.3 92.3 - - + +
144C SER* 1.3 61.9 + - - +
145C ILE* 5.0 0.2 - - + -
1174C GOL 3.0 5.0 + - - -
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Residues in contact with SER 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS* 3.5 20.9 + - - +
103C VAL 3.1 6.9 + - - -
104C THR* 3.1 26.7 + - - +
105C VAL* 2.7 33.8 - - - -
143C ILE* 1.3 74.3 - - - +
145C ILE* 1.3 56.4 + - - +
146C VAL* 5.0 4.3 - - - +
1174C GOL 3.3 16.2 + - - -
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Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ARG* 5.5 0.2 - - - +
244B ARG* 3.5 55.4 + - + +
105C VAL* 3.3 10.8 - - + +
123C GLU* 4.1 36.6 - - + +
126C ALA* 3.9 28.0 - - + +
127C ASN* 4.5 2.0 - - - +
130C LYS* 4.3 25.6 - - + -
143C ILE* 4.8 1.1 - - + +
144C SER* 1.3 76.9 + - - +
146C VAL* 1.3 66.6 + - - +
147C SER 4.9 2.0 - - - +
1174C GOL 3.1 17.9 + - - -
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Residues in contact with VAL 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE* 4.0 18.2 - - + -
222B GLY 3.7 21.5 - - - +
223B ARG* 4.3 19.1 - - + -
224B SER 4.9 0.9 - - - +
244B ARG* 5.5 3.8 - - - +
104C THR* 4.1 20.9 - - + -
105C VAL 2.9 9.1 + - - +
106C GLU* 3.3 7.2 - - + +
107C GLY 3.1 18.5 + - - -
126C ALA* 5.4 0.2 - - - -
144C SER* 5.0 5.2 - - - +
145C ILE* 1.3 79.9 - - - +
147C SER* 1.3 60.4 + - - +
148C TYR* 3.7 30.7 + - + +
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE* 3.5 20.4 - - - -
244B ARG* 5.9 2.6 - - - +
245B HIS* 4.6 2.9 + - - +
107C GLY* 3.6 6.7 - - - +
119C ILE* 2.9 42.0 + - - +
122C GLY* 3.4 9.9 - - - -
123C GLU* 3.5 29.1 + - - +
126C ALA* 6.0 0.2 - - - -
145C ILE* 4.1 2.4 - - - +
146C VAL* 1.3 72.3 - - - +
148C TYR* 1.3 59.6 + - - +
149C GLY 3.0 15.1 + - - -
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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