Contacts of the strand formed by residues 140 - 144 (chain A) in PDB entry 3GGE
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 PHE 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ILE* 3.4 6.7 - - - -
132A THR* 2.8 59.7 + - + +
133A ASP* 4.3 16.4 - - - -
134A ASN* 4.9 3.4 - - + -
138A TYR 4.2 4.0 - - - -
139A ALA* 1.3 76.1 - - - +
141A ILE* 1.3 75.1 + - - +
142A LYS* 4.9 5.6 - - + -
159A GLY* 4.1 10.5 - - - +
160A ASP 3.2 16.2 - - - +
161A HIS* 3.8 36.6 - + + +
162A ILE* 4.6 2.7 - - - +
199B LYS* 5.5 4.5 - - + -
174C ARG* 5.8 13.2 - - + -
176C TYR* 5.4 2.0 - - - -
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Residues in contact with ILE 141 (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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129A LEU* 4.4 20.6 - - + -
130A THR 3.6 6.5 - - - +
131A ILE* 4.7 0.9 - - + +
140A PHE* 1.3 79.3 - - - +
142A LYS* 1.3 60.9 + - - +
143A ARG 3.5 22.0 - - - +
144A ILE* 3.8 18.6 - - + -
156A ILE* 3.4 31.9 - - + -
157A CYS 4.0 11.9 - - - +
158A VAL* 3.7 4.9 - - - +
159A GLY* 2.9 21.1 + - - -
160A ASP* 3.0 21.3 + - + +
162A ILE* 4.3 20.0 - - + -
193A MET* 6.4 0.7 - - - -
195A LEU* 5.0 3.6 - - + -
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Residues in contact with LYS 142 (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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130A THR* 2.9 19.4 + - + +
132A THR* 4.1 23.1 - - + -
140A PHE* 3.6 7.9 + - + -
141A ILE* 1.3 74.3 - - - +
143A ARG* 1.3 96.0 + - + +
158A VAL* 3.7 18.5 - - - +
2B SO4 4.8 19.7 + - - -
199B LYS 5.0 6.3 + - - -
201B SER* 4.4 24.5 + - - -
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Residues in contact with ARG 143 (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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129A LEU* 3.5 3.1 - - - -
130A THR* 3.0 48.7 + - - +
141A ILE* 3.5 9.6 - - - +
142A LYS* 1.3 119.8 - - - +
144A ILE* 1.3 67.2 + - - +
145A LYS 4.2 0.4 - - - +
158A VAL* 4.4 3.6 - - - -
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Residues in contact with ILE 144 (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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128A GLY 3.7 7.0 - - - +
129A LEU* 4.9 0.9 - - + -
141A ILE* 3.8 12.8 - - + -
143A ARG* 1.3 81.9 - - - +
145A LYS* 1.3 63.3 + - - +
146A ASP* 3.5 8.0 + - - +
150A ILE* 4.2 16.6 - - + +
151A ASP* 3.6 43.1 - - + +
156A ILE* 3.8 22.4 - - + +
157A CYS* 3.9 3.4 - - - -
158A VAL* 3.7 34.2 - - + +
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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