Contacts of the helix formed by residues 1397 - 1410 (chain J) in PDB entry 4XLR
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 LYS1397 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1192J LEU 5.1 8.9 + - - -
1341J PRO* 6.3 1.0 - - - +
1345J GLU* 5.5 1.2 + - - -
1373J ARG* 5.5 2.8 - - + +
1376J LEU* 3.7 35.3 - - + +
1377J LYS* 2.4 39.2 + - + +
1379J VAL* 4.5 14.1 - - + -
1396J GLU* 1.3 66.1 - - - +
1398J TRP* 1.3 71.3 + - + +
1400J VAL* 3.0 10.8 - - + +
1401J GLU* 2.9 48.3 + - - +
1417J TRP* 5.4 9.2 - - + -
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Residues in contact with TRP1398 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104J GLU* 3.8 2.9 - - - -
1105J ILE* 3.8 15.9 - - + -
1194J CYS 5.6 1.8 + - - -
1195J GLN* 5.7 2.7 - - - -
1196J THR 4.7 1.6 + - - -
1197J ARG* 3.3 41.5 + - + +
1198J TYR* 3.4 52.5 - + - -
1373J ARG* 3.4 35.5 - - - +
1374J GLN* 3.7 6.5 - - - -
1377J LYS* 3.3 32.4 - - + +
1396J GLU* 3.3 26.2 - - + -
1397J LYS* 1.3 89.4 - - + +
1399J ASP* 1.3 60.5 + - - +
1401J GLU* 3.1 9.5 - - - +
1402J ALA* 3.0 26.5 + - - +
1432J LYS* 5.0 0.2 - - - -
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Residues in contact with ASP1399 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197J ARG* 3.0 24.1 + - - +
1198J TYR* 3.6 8.7 + - - -
1395J LEU* 3.8 17.6 - - + +
1396J GLU* 3.3 15.1 + - - +
1397J LYS 3.4 0.4 - - - -
1398J TRP* 1.3 72.6 - - - +
1400J VAL* 1.3 61.0 + - - +
1402J ALA* 3.2 6.9 + - - +
1403J LEU* 2.9 28.9 + - - +
1406J ARG* 5.2 0.5 + - - -
1432J LYS* 3.0 24.1 + - - -
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Residues in contact with VAL1400 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379J VAL* 3.6 21.3 - - + -
1381J VAL* 5.9 1.3 - - + -
1389J LEU* 5.0 2.2 - - + -
1395J LEU* 3.6 17.9 - - + +
1396J GLU 3.2 15.5 + - - +
1397J LYS* 3.0 20.9 - - + +
1399J ASP* 1.3 77.9 - - - +
1401J GLU* 1.3 57.4 + - - +
1403J LEU* 4.0 18.8 - - + -
1404J ASN* 2.9 34.8 + - - +
1415J VAL* 4.8 5.4 - - + -
1417J TRP* 3.7 37.9 - - + +
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Residues in contact with GLU1401 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195J GLN* 5.3 8.3 - - - +
1197J ARG* 6.5 0.2 - - - -
1397J LYS* 2.9 39.6 + - - +
1398J TRP* 3.1 13.8 - - - +
1399J ASP 3.1 0.2 - - - -
1400J VAL* 1.3 78.3 - - - +
1402J ALA* 1.3 64.4 - - - +
1404J ASN* 3.3 6.9 + - - +
1405J GLU* 3.0 40.7 + - + +
1417J TRP* 3.8 24.9 - - - -
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Residues in contact with ALA1402 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197J ARG* 5.3 9.9 - - - +
1398J TRP 3.0 13.2 + - - +
1399J ASP* 3.2 10.7 + - - +
1401J GLU* 1.3 73.6 - - - +
1403J LEU* 1.3 65.7 + - - +
1405J GLU* 3.1 14.7 + - - +
1406J ARG* 2.9 38.3 + - + +
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Residues in contact with LEU1403 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1387J SER* 4.1 7.9 - - - -
1388J ARG 5.6 0.7 - - - +
1389J LEU* 3.7 34.3 - - + -
1395J LEU* 5.8 1.6 - - + -
1399J ASP 2.9 13.0 + - - +
1400J VAL* 3.4 19.7 - - + +
1402J ALA* 1.3 76.2 - - - +
1404J ASN* 1.3 65.3 + - - +
1406J ARG* 3.2 26.2 + - - +
1407J LEU* 2.9 56.6 + - + +
1415J VAL* 3.7 20.4 - - + -
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Residues in contact with ASN1404 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400J VAL* 2.9 27.3 + - - +
1401J GLU* 3.6 7.7 + - - +
1403J LEU* 1.3 72.9 - - - +
1405J GLU* 1.3 64.0 + - + +
1407J LEU* 3.3 6.2 + - - +
1408J ILE* 2.9 30.7 + - + +
1414J PRO* 3.3 11.1 - - + +
1415J VAL* 2.7 41.5 + - - +
1417J TRP* 3.0 34.4 - - - +
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Residues in contact with GLU1405 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195J GLN* 5.5 2.8 - - - +
1401J GLU* 3.0 39.1 + - + +
1402J ALA* 3.4 11.2 + - - +
1404J ASN* 1.3 75.5 - - + +
1406J ARG* 1.3 64.3 + - + +
1408J ILE* 3.0 20.0 + - - +
1409J ALA* 3.0 13.4 + - - +
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Residues in contact with ARG1406 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1399J ASP 5.2 0.4 + - - -
1402J ALA* 2.9 26.5 + - + +
1403J LEU* 3.4 47.1 - - - +
1405J GLU* 1.3 76.4 - - + +
1407J LEU* 1.3 68.1 + - - +
1409J ALA* 3.1 8.5 + - - +
1410J GLU* 3.0 37.6 + - - +
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Residues in contact with LEU1407 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1386J ASP* 4.5 1.3 - - + -
1387J SER* 3.7 33.9 - - - +
1403J LEU* 2.9 40.2 + - + +
1404J ASN* 3.7 5.6 - - - +
1406J ARG* 1.3 82.1 - - - +
1408J ILE* 1.3 63.5 + - - +
1410J GLU* 3.3 18.6 + - - +
1411J GLY 3.3 3.3 + - - -
1412J LYS* 2.8 52.6 + - + +
1413J VAL 3.6 19.7 - - - +
1414J PRO* 4.3 8.3 - - + -
1415J VAL* 4.7 0.4 - - + -
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Residues in contact with ILE1408 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1404J ASN* 2.9 26.6 + - + +
1405J GLU* 3.0 10.7 + - - +
1407J LEU* 1.3 76.4 - - - +
1409J ALA* 1.3 63.5 + - - +
1411J GLY* 3.3 12.8 + - - -
1412J LYS 4.2 2.2 - - - +
1414J PRO* 3.7 36.8 - - + -
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Residues in contact with ALA1409 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405J GLU 3.0 10.7 + - - +
1406J ARG* 3.1 11.6 + - - +
1408J ILE* 1.3 80.1 - - - +
1410J GLU* 1.3 59.3 + - + +
1411J GLY* 3.1 4.7 + - - -
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Residues in contact with GLU1410 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406J ARG* 3.0 35.8 + - - +
1407J LEU* 3.5 23.4 - - - +
1408J ILE 3.3 0.2 - - - -
1409J ALA* 1.3 76.5 - - + +
1411J GLY* 1.3 60.6 + - - +
1412J LYS* 3.6 38.7 + - + +
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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