Contacts of the helix formed by residues 1249 - 1254 (chain A) in PDB entry 3PLS
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 LEU1249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1238A TYR 5.4 2.5 - - - +
1240A SER 4.5 6.7 - - - +
1241A VAL* 5.9 0.2 - - - -
1242A GLN 5.5 1.1 - - - +
1243A GLN* 3.4 36.3 - - + +
1245A ARG 4.0 6.7 - - - +
1246A HIS* 3.4 37.8 + - + +
1247A ALA 3.8 0.2 - - - -
1248A ARG* 1.3 79.9 - - - +
1250A PRO* 1.3 78.2 - - + +
1251A VAL* 3.2 12.1 - - + +
1252A LYS* 3.1 15.0 + - + +
1253A TRP* 3.2 12.6 - - - -
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Residues in contact with PRO1250 (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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1208A ASP* 4.1 9.4 - - - +
1212A ARG* 4.2 10.1 - - - +
1238A TYR* 3.5 56.1 - - + +
1239A TYR* 3.8 23.6 - - + -
1248A ARG 4.4 1.8 - - - +
1249A LEU* 1.3 89.9 - - + +
1251A VAL* 1.3 57.3 + - - +
1252A LYS 3.0 0.2 - - - -
1253A TRP* 2.9 21.7 + - + +
1254A THR* 2.7 23.8 + - + +
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Residues in contact with VAL1251 (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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1238A TYR 5.1 0.2 - - - +
1239A TYR* 3.2 33.3 - - - +
1240A SER 3.3 21.5 - - - +
1241A VAL* 4.5 13.2 - - + +
1249A LEU* 4.5 10.8 - - + +
1250A PRO* 1.3 77.8 - - - +
1252A LYS* 1.3 63.1 + - + +
1253A TRP 3.1 1.4 + - - -
1254A THR* 3.4 23.5 + - - +
1259A LEU* 3.9 21.6 - - + +
1293A PRO 5.6 2.5 - - - +
1296A LEU* 3.7 24.4 - - + +
1300A LEU* 6.1 0.2 - - - +
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Residues in contact with LYS1252 (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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1246A HIS* 3.3 34.7 - - + +
1247A ALA* 3.0 33.3 + - - +
1249A LEU* 3.1 12.0 + - + +
1250A PRO 3.0 1.2 + - - -
1251A VAL* 1.3 80.8 - - + +
1253A TRP* 1.3 67.8 + - + +
1254A THR 3.6 0.4 - - - -
1271A TRP* 5.3 0.9 + - - -
1275A VAL* 4.0 10.7 - - - +
1286A PRO* 4.7 0.4 - - - +
1287A PRO* 2.9 27.2 + - + +
1288A TYR* 3.3 49.7 + - + -
1289A ARG* 3.7 12.3 + - - +
1291A ILE 4.9 2.5 - - - -
1293A PRO* 6.2 1.1 - - - -
1296A LEU* 4.0 23.8 - - + -
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Residues in contact with TRP1253 (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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1208A ASP* 5.9 2.9 - - - +
1209A LEU 3.5 25.4 - - - +
1210A ALA* 3.6 16.2 - - + +
1212A ARG* 5.9 7.4 - - - -
1248A ARG* 3.9 37.7 - - + -
1249A LEU 3.2 29.4 - - - -
1250A PRO* 2.9 12.7 + - + +
1252A LYS* 1.3 89.0 - - + +
1254A THR* 1.3 61.0 + - + +
1271A TRP* 3.3 11.1 - - - -
1272A SER* 2.8 34.4 + - - +
1275A VAL* 3.4 28.8 - - + +
1276A LEU 4.4 0.2 - - - -
1279A GLU* 3.0 41.5 + - - -
1287A PRO* 3.5 24.7 - - + -
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Residues in contact with THR1254 (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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1207A ARG 3.9 9.0 - - - +
1208A ASP* 5.6 1.8 - - - -
1239A TYR* 3.7 31.2 - - + -
1250A PRO* 2.7 17.6 + - + +
1251A VAL* 3.4 16.6 + - - +
1252A LYS 3.6 0.5 - - - -
1253A TRP* 1.3 80.8 - - + +
1255A ALA* 1.3 69.3 + - - +
1256A LEU 3.7 0.7 + - - -
1258A SER* 5.0 1.3 - - - -
1259A LEU* 3.5 23.7 - - - +
1264A PHE* 3.7 20.2 - - + -
1268A SER* 5.8 1.1 - - - +
1271A TRP* 3.7 10.4 + - - -
1272A SER* 4.2 9.0 - - - +
1300A LEU* 5.2 1.7 - - - +
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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