Contacts of the strand formed by residues 140 - 144 (chain C) in PDB entry 4IYM
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 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C VAL* 4.2 6.5 - - + +
48C ALA* 4.0 16.8 - - + +
49C LYS* 3.4 44.4 - - + +
52C GLN* 4.9 3.8 - - + -
138C VAL* 4.0 5.9 + - - -
139C GLY* 1.3 80.0 - - - +
141C GLY* 1.3 70.1 + - - +
167C ALA* 3.4 11.2 - - + +
169C ILE* 4.1 22.2 - - + -
215C ASP* 3.8 20.3 + - + +
216C ILE* 3.6 10.8 - - + -
217C ALA* 3.0 28.3 + - - +
218C ALA 3.9 1.6 + - - -
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Residues in contact with GLY 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C VAL* 5.1 2.4 - - - +
139C GLY 4.3 0.6 - - - -
140C ILE* 1.3 80.1 - - - +
142C ALA* 1.3 60.9 + - - +
161C ALA* 5.9 1.6 - - - -
166C ASN* 4.8 3.9 - - - +
167C ALA 2.9 10.8 + - - -
168C PHE* 3.4 14.2 - - - -
169C ILE* 2.9 22.3 + - - +
216C ILE* 4.2 2.0 - - - -
218C ALA* 3.4 16.8 - - - -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C GLY* 1.3 75.3 - - - +
143C GLY* 1.3 59.5 + - - +
144C ILE* 5.9 0.2 - - + -
168C PHE* 3.7 10.4 - - - -
169C ILE* 3.0 20.6 - - + +
210C ILE* 3.6 35.2 - - + -
216C ILE* 4.0 12.3 - - + -
218C ALA 3.0 7.0 + - - +
219C VAL* 3.3 7.7 - - + +
220C SER* 3.0 22.3 + - - -
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Residues in contact with GLY 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ALA* 1.3 74.6 - - - +
144C ILE* 1.3 61.5 + - - +
157C MSE 3.6 10.1 - - - -
168C PHE* 3.3 18.7 - - - -
169C ILE 2.9 6.9 + - - +
170C LEU* 3.6 6.9 - - - +
171C LYS* 2.8 32.4 + - - +
220C SER* 3.1 9.4 - - - -
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLY* 1.3 78.0 - - - +
145C THR* 1.3 66.7 + - - +
157C MSE 3.6 2.8 - - - +
171C LYS* 3.4 22.4 - - + +
207C VAL* 3.8 44.0 - - + -
210C ILE* 4.5 12.3 - - + -
211C LEU* 4.7 3.6 - - + -
219C VAL* 3.9 25.8 - - + -
220C SER 2.9 6.6 + - - +
221C PHE* 3.4 24.7 - - + -
222C VAL 3.0 26.6 + - - +
231C VAL* 4.2 13.0 - - + -
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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