Contacts of the helix formed by residues 1248 - 1262 (chain A) in PDB entry 5TJ4
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 ASN1248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246A SER 4.3 0.6 + - - -
1247A ARG* 1.3 75.8 - - - +
1249A MET* 1.3 62.3 + - - +
1250A LYS* 2.4 39.6 + - - +
1251A GLU* 2.7 28.4 - - + +
1252A LYS* 3.0 25.1 + - - +
1371A ASP 4.8 2.6 + - - -
1374A ALA* 3.2 35.3 + - - +
1375A SER* 4.4 17.1 + - - +
1377A PRO* 5.1 2.0 - - - +
137B LYS* 5.4 3.2 - - + +
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Residues in contact with MET1249 (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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1247A ARG 3.8 1.4 + - - -
1248A ASN* 1.3 73.9 + - - +
1250A LYS* 1.3 62.5 + - - +
1251A GLU 3.1 1.8 - - - -
1252A LYS* 3.3 34.6 + - + +
1253A LEU* 3.1 23.9 + - - +
1256A MET* 5.9 1.3 - - - -
1331A ASP 5.6 2.7 - - - +
1335A ALA* 4.9 10.5 - - + -
1370A TRP* 3.9 21.1 - - + -
1374A ALA* 4.3 10.3 - - + +
1390A CYS* 4.3 23.3 - - + -
1391A ALA* 5.4 1.6 - - - +
1394A VAL* 3.5 29.2 - - + -
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Residues in contact with LYS1250 (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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1248A ASN* 2.4 30.1 + - - +
1249A MET* 1.3 69.9 - - - +
1251A GLU* 1.3 60.0 + - + +
1253A LEU* 3.8 1.9 + - - +
1254A GLU* 3.2 33.7 + - - +
1370A TRP* 3.6 40.8 + - + +
1371A ASP* 4.8 6.7 - - - -
1374A ALA* 4.0 9.0 - - + +
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Residues in contact with GLU1251 (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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1247A ARG* 5.1 6.5 - - + -
1248A ASN* 2.7 49.8 - - + +
1250A LYS* 1.3 75.4 - - + +
1252A LYS* 1.3 65.9 + - - +
1254A GLU* 3.0 16.8 + - - +
1255A ASP* 2.9 30.8 + - - +
137B LYS* 6.0 5.2 - - + -
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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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1245A ASP* 3.9 26.8 - - - +
1247A ARG* 3.7 41.4 - - + +
1248A ASN 3.0 14.8 + - - +
1249A MET* 3.5 38.8 - - + +
1251A GLU* 1.3 75.7 - - - +
1253A LEU* 1.3 57.9 + - - +
1255A ASP* 3.3 3.3 + - - +
1256A MET* 2.9 35.9 + - - +
1327A LYS* 5.4 0.6 - - - +
1331A ASP* 3.8 38.1 + - + +
1334A ASP* 5.8 4.6 - - - +
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Residues in contact with LEU1253 (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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1249A MET 3.1 13.3 + - - +
1250A LYS 4.0 3.4 - - - +
1252A LYS* 1.3 76.5 - - - +
1254A GLU* 1.3 58.8 - - + +
1256A MET* 3.1 6.2 + - - +
1257A GLU* 2.8 53.6 + - + +
1359A LYS* 5.8 0.9 - - - +
1370A TRP* 4.2 13.9 - - + +
1393A TYR* 3.7 31.9 - - + +
1394A VAL* 4.1 24.2 - - + +
1397A SER* 4.0 22.0 - - - +
1398A ILE* 3.9 27.6 - - + -
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Residues in contact with GLU1254 (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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1250A LYS* 3.2 22.3 + - - +
1251A GLU* 3.0 18.3 + - - +
1253A LEU* 1.3 77.9 - - + +
1255A ASP* 1.3 59.2 + - - +
1257A GLU* 4.0 9.1 + - - +
1258A SER* 3.1 28.8 + - - -
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Residues in contact with ASP1255 (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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1247A ARG* 3.3 29.0 + - - +
1251A GLU* 2.9 20.1 + - - +
1252A LYS 3.5 7.4 - - - +
1254A GLU* 1.3 75.8 - - - +
1256A MET* 1.3 66.9 + - + +
1258A SER* 3.1 9.2 + - - -
1259A VAL* 3.1 30.1 + - + +
137B LYS 4.9 1.9 - - - +
138B GLU* 5.8 0.7 - - - -
141B ALA* 3.7 13.7 - - + +
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Residues in contact with MET1256 (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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1247A ARG* 6.0 0.7 - - - +
1249A MET* 5.9 1.1 - - - -
1252A LYS* 2.9 30.1 + - - +
1253A LEU* 3.6 9.9 - - - +
1255A ASP* 1.3 75.3 - - + +
1257A GLU* 1.3 63.0 + - - +
1259A VAL* 3.3 4.5 + - - +
1260A LEU* 3.2 28.9 + - + +
1328A ALA* 3.4 27.5 - - + +
1331A ASP* 3.5 26.7 - - - +
1332A PHE* 3.3 39.9 - - + +
1394A VAL* 4.2 13.2 - - + -
1398A ILE* 3.8 26.2 - - + -
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Residues in contact with GLU1257 (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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1253A LEU* 2.8 43.3 + - + +
1254A GLU* 4.0 7.7 + - - +
1256A MET* 1.3 71.8 - - - +
1258A SER* 1.3 56.7 + - - +
1260A LEU* 3.5 4.0 + - - +
1261A LYS* 3.0 30.7 + - - +
1359A LYS* 4.3 8.4 + - - -
1397A SER* 3.9 22.2 - - - +
1398A ILE* 4.1 18.8 - - + -
1401A GLU* 3.8 29.9 - - + +
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Residues in contact with SER1258 (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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1254A GLU 3.1 15.7 + - - -
1255A ASP* 3.4 12.3 - - - -
1257A GLU* 1.3 74.5 - - - +
1259A VAL* 1.3 65.6 + - - +
1261A LYS* 3.5 16.8 + - - +
1262A ASP* 3.6 14.9 + - - +
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Residues in contact with VAL1259 (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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1255A ASP* 3.1 17.6 + - + +
1256A MET* 3.3 7.8 + - - +
1258A SER* 1.3 79.3 - - - +
1260A LEU* 1.3 65.1 + - + +
1261A LYS 3.5 0.5 + - - -
1262A ASP* 3.5 20.3 + - - +
1263A LEU* 4.1 4.0 - - - +
1322A VAL* 5.4 2.0 - - + -
1324A ALA* 3.9 27.1 - - + +
1325A ARG* 3.4 45.6 + - + +
1328A ALA* 4.6 4.5 - - + -
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Residues in contact with LEU1260 (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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1256A MET* 3.2 17.9 + - + +
1257A GLU* 4.1 4.5 - - - +
1259A VAL* 1.3 83.1 - - + +
1261A LYS* 1.3 65.6 + - - +
1262A ASP 3.4 0.2 - - - -
1263A LEU* 3.5 34.4 - - + +
1268A ARG* 4.1 11.8 - - - +
1271A VAL* 5.5 3.1 - - + -
1325A ARG* 5.3 3.6 - - + +
1328A ALA* 4.5 14.4 - - + -
1329A ILE* 4.6 19.5 - - + -
1398A ILE* 3.7 36.6 - - + +
1401A GLU* 4.9 10.3 - - + +
1402A LEU* 4.0 26.6 - - + +
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Residues in contact with LYS1261 (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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1257A GLU 3.0 18.4 + - - +
1258A SER* 3.6 10.1 - - - +
1260A LEU* 1.3 77.5 - - - +
1262A ASP* 1.3 62.3 + - - +
1263A LEU 2.9 13.2 + - - +
1268A ARG* 5.1 4.2 - - - +
1401A GLU* 4.1 14.7 + - - +
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Residues in contact with ASP1262 (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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1258A SER* 3.6 13.4 + - - +
1259A VAL* 3.5 12.0 + - - +
1260A LEU 3.4 0.4 - - - -
1261A LYS* 1.3 77.2 - - - +
1263A LEU* 1.3 65.3 + - - +
1325A ARG* 4.0 12.6 + - - -
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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