Contacts of the helix formed by residues 1297 - 1310 (chain I) in PDB entry 6C6U
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 ASP1297 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292I THR* 2.9 25.4 + - + +
1296I ASP* 1.3 70.9 - - - +
1298I VAL* 1.3 65.1 + - - +
1299I ASN* 3.8 10.5 + - - +
1300I GLY* 3.7 14.0 + - - +
1301I ARG* 2.8 32.0 + - - +
1317I PRO 2.8 24.7 - - - +
1318I GLY* 3.3 14.6 - - - -
1319I MET 3.2 24.6 + - - +
1321I GLU* 4.9 5.2 + - - +
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Residues in contact with VAL1298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256I GLN* 5.2 12.1 - - + +
1296I ASP 3.2 4.2 + - - +
1297I ASP* 1.3 73.0 + - - +
1299I ASN* 1.3 75.6 + - - +
1301I ARG* 3.3 33.1 + - - +
1302I THR* 3.0 31.4 + - + +
1321I GLU* 5.2 12.5 - - + +
96J LYS* 3.9 24.5 - - - +
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Residues in contact with ASN1299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1297I ASP* 3.8 6.6 + - - +
1298I VAL* 1.3 87.8 - - - +
1300I GLY* 1.3 58.1 + - - +
1302I THR* 3.1 9.1 + - - -
1303I LYS* 3.0 38.8 + - + +
96J LYS* 4.8 11.0 + - - +
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Residues in contact with GLY1300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293I VAL* 4.3 9.3 - - - +
1297I ASP* 3.4 22.6 + - - -
1298I VAL 3.3 0.6 - - - -
1299I ASN* 1.3 79.0 - - - +
1301I ARG* 1.3 56.7 + - - +
1303I LYS* 3.5 6.0 + - - +
1304I MET* 2.9 27.6 + - - +
1316I GLU* 3.8 23.9 + - - +
1317I PRO 4.7 0.4 - - - -
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Residues in contact with ARG1301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251I TYR* 3.2 61.6 - - - -
1256I GLN* 3.6 26.3 + - - -
1293I VAL 3.4 21.9 + - - +
1294I LYS* 5.3 0.7 - - - -
1295I SER 3.7 4.9 + - - -
1296I ASP 2.7 37.0 + - - -
1297I ASP 2.8 17.3 + - - +
1298I VAL* 3.3 30.1 + - - +
1300I GLY* 1.3 71.8 - - - +
1302I THR* 1.3 64.6 + - + +
1304I MET* 3.5 8.5 - - + +
1305I TYR* 2.9 27.0 + - - +
348J ASP* 4.5 2.2 - - - -
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Residues in contact with THR1302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298I VAL* 3.0 21.8 + - + +
1299I ASN* 3.1 20.8 + - - +
1301I ARG* 1.3 78.9 - - + +
1303I LYS* 1.3 64.8 + - - +
1305I TYR* 3.3 5.8 + - - +
1306I LYS* 3.1 37.0 + - - +
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Residues in contact with LYS1303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299I ASN* 3.0 24.1 + - + +
1300I GLY* 3.7 6.1 - - - +
1302I THR* 1.3 78.2 + - - +
1304I MET* 1.3 57.7 + - - +
1306I LYS* 3.5 16.5 + - + +
1307I ASN* 3.0 41.1 + - - +
1316I GLU* 3.4 43.4 + - + +
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Residues in contact with MET1304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1289I GLU* 5.0 1.1 - - - +
1293I VAL* 3.6 28.7 - - + -
1300I GLY 2.9 18.0 + - - +
1301I ARG* 3.5 7.4 - - + +
1302I THR 3.2 0.2 - - - -
1303I LYS* 1.3 78.1 - - - +
1305I TYR* 1.3 57.9 + - - +
1307I ASN* 3.3 4.1 + - + +
1308I ILE* 2.8 64.9 + - + +
1314I GLN 3.2 33.7 - - - +
1315I MET* 4.0 10.5 - - - +
1316I GLU 6.0 0.2 - - - +
349J TYR* 5.8 2.2 - - + +
472J LEU* 3.9 30.7 - - + -
473J THR* 4.3 11.7 - - - +
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Residues in contact with TYR1305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248I THR* 4.7 15.5 - - + -
1301I ARG 2.9 17.8 + - - +
1302I THR* 3.3 6.7 + - - +
1304I MET* 1.3 76.3 - - - +
1306I LYS* 1.3 67.3 + - + +
1308I ILE* 3.4 3.4 + - - +
1309I VAL* 3.0 40.2 + - + +
349J TYR* 3.8 18.6 - - - +
379J PRO* 3.6 25.4 - - + -
382J TYR* 3.3 29.0 - + - -
394J ILE* 4.6 10.0 - - + +
398J LYS* 5.4 3.6 + - - -
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Residues in contact with LYS1306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1302I THR* 3.1 25.8 + - - +
1303I LYS* 3.9 18.1 - - + +
1305I TYR* 1.3 78.9 - - + +
1307I ASN* 1.3 58.5 + - - +
1309I VAL* 3.4 10.1 - - + +
1310I ASP* 3.0 38.9 + - - +
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Residues in contact with ASN1307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303I LYS* 3.0 33.2 + - - +
1304I MET* 3.7 4.0 - - - +
1306I LYS* 1.3 76.9 - - - +
1308I ILE* 1.3 61.0 + - + +
1310I ASP* 3.6 3.9 + - - +
1311I GLY 3.2 2.6 + - - -
1312I ASN* 2.9 67.2 + - - +
1314I GLN* 3.6 25.5 + - - +
1315I MET* 5.4 0.4 - - - +
1316I GLU* 5.2 9.7 + - - +
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Residues in contact with ILE1308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1304I MET* 2.8 49.7 + - + +
1305I TYR* 4.0 4.7 - - - +
1306I LYS 3.3 0.2 - - - -
1307I ASN* 1.3 79.3 - - - +
1309I VAL* 1.3 61.2 + - - +
1311I GLY* 3.2 13.0 + - - -
1313I HIS* 3.5 33.6 - - + +
349J TYR* 5.3 3.4 - - - +
379J PRO* 3.6 36.4 - - + +
380J PHE* 4.0 25.4 - - + +
383J GLY* 4.7 2.8 - - - -
472J LEU* 4.3 15.0 - - + +
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Residues in contact with VAL1309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305I TYR* 3.0 38.5 + - + +
1306I LYS* 3.4 14.6 - - + +
1308I ILE* 1.3 75.0 - - - +
1310I ASP* 1.3 63.2 + - - +
1311I GLY 3.5 0.2 - - - -
379J PRO* 3.8 29.8 - - + +
382J TYR* 4.0 16.2 - - + -
383J GLY* 3.5 17.2 - - - +
386J GLU* 3.2 28.8 - - - +
394J ILE* 4.5 6.7 - - + -
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Residues in contact with ASP1310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306I LYS* 3.0 25.8 + - - +
1307I ASN* 3.6 5.1 + - - +
1308I ILE 3.1 0.2 - - - -
1309I VAL* 1.3 87.5 - - - +
1311I GLY* 1.3 58.9 + - - +
1312I ASN* 3.4 6.5 + - + +
383J GLY* 5.9 0.4 - - - -
386J GLU* 4.0 8.3 - - - +
387J LEU* 6.1 0.5 - - - +
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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