Contacts of the strand formed by residues 1214 - 1217 (chain B) in PDB entry 1G24
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 GLU1214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079B TYR* 4.1 5.9 - - - -
1080B THR* 4.7 2.2 - - - +
1174B SER* 2.7 33.3 + - - -
1175B THR 3.2 14.8 - - - +
1176B SER* 4.8 0.2 - - - -
1202B TYR* 3.5 5.5 - - - -
1203B ILE* 3.1 54.3 + - + +
1204B ASP* 3.7 5.2 + - - +
1210B ALA* 3.4 9.5 - - + -
1211B GLY* 2.7 46.8 + - - +
1212B GLN 3.1 2.2 - - - -
1213B LEU* 1.3 77.6 - - - +
1215B MET* 1.3 66.1 + - - +
1216B LEU* 4.2 1.6 - - - +
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Residues in contact with MET1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058B TRP* 4.1 15.0 - - + -
1062B GLN* 6.3 0.7 - - + -
1066B TYR* 5.4 1.3 - - - +
1120B THR* 4.8 2.9 - - - -
1124B ILE* 3.8 26.9 - - + -
1126B LEU* 3.8 11.4 - - + -
1173B ILE 3.8 0.9 - - - +
1175B THR* 2.8 49.6 + - - +
1177B LEU* 3.3 31.2 - - + +
1200B ALA* 4.0 26.9 - - + +
1201B GLY 3.2 4.7 - - - +
1202B TYR* 3.5 37.7 - - + +
1213B LEU 3.3 0.9 + - - +
1214B GLU* 1.3 74.5 - - - +
1216B LEU* 1.3 63.1 + - - +
1217B LEU* 4.7 0.8 - - - +
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Residues in contact with LEU1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076B ILE* 5.5 3.8 - - + -
1079B TYR* 3.6 47.6 - - + +
1111B LEU* 5.1 11.7 - - + -
1115B PHE* 3.2 24.1 - - + -
1118B MET* 6.0 1.3 - - + -
1172B TYR* 3.9 15.7 - - + -
1173B ILE 3.7 10.5 - - - +
1174B SER* 3.6 13.2 - - - +
1200B ALA* 3.4 3.1 - - - -
1201B GLY 2.7 37.7 + - - +
1203B ILE* 4.0 25.1 - - + +
1214B GLU* 4.0 2.5 - - - +
1215B MET* 1.3 73.1 - - - +
1217B LEU* 1.3 65.8 + - - +
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Residues in contact with LEU1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115B PHE* 3.6 2.7 - - - -
1126B LEU* 3.9 21.1 - - + -
1172B TYR* 3.6 9.5 - - - +
1173B ILE* 2.9 42.5 + - + +
1175B THR* 4.1 20.6 - - + -
1192B PHE* 4.9 2.5 - - + -
1194B VAL* 4.7 11.4 - - + -
1199B LYS 3.6 19.1 - - - +
1200B ALA* 3.7 18.2 - - + -
1215B MET 4.7 0.4 - - - +
1216B LEU* 1.3 75.3 - - - +
1218B PRO* 1.3 76.4 - - + +
1221B SER* 5.2 1.8 - - - +
1243B MET* 3.7 35.0 - - + -
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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
------------------------------------------------------------
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