Contacts of the helix formed by residues 1395 - 1407 (chain D) in PDB entry 2O5J
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 LEU1395 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1376D MET 3.4 21.3 - - - +
1377D LYS* 2.7 32.6 + - + +
1378D TYR 4.2 0.9 - - - +
1379D VAL* 4.0 22.2 - - + -
1393D GLN 3.2 3.4 + - - -
1394D VAL* 1.3 67.4 - - - +
1396D GLU* 1.3 84.4 + - + +
1398D TRP* 2.8 36.2 + - - +
1399D ASP* 3.2 17.7 + - - +
1417D TRP* 5.7 7.6 - - + +
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Residues in contact with GLU1396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195D GLN 4.4 8.5 - - - +
1197D ARG* 3.2 52.9 + - + +
1198D TYR* 5.7 1.3 - - + -
1377D LYS* 5.4 2.0 - - + +
1394D VAL* 3.3 8.5 - - + +
1395D LEU* 1.3 89.5 - - + +
1397D LYS* 1.3 63.5 + - - +
1399D ASP* 2.9 36.6 + - - +
1400D VAL* 3.2 20.7 + - - +
1403D LEU* 6.1 0.7 - - - +
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Residues in contact with LYS1397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197D ARG* 4.0 25.4 - - - +
1198D TYR* 5.0 6.5 - - - -
1393D GLN* 3.4 24.7 - - - +
1394D VAL* 2.7 33.1 + - + +
1396D GLU* 1.3 76.7 + - - +
1398D TRP* 1.3 61.3 + - + +
1400D VAL* 3.4 36.2 - - + +
1401D GLU* 3.4 9.2 + - - +
1432D LYS* 5.8 6.5 - - + +
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Residues in contact with TRP1398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379D VAL* 3.3 27.6 - - + +
1381D VAL* 3.5 35.7 - - + -
1386D ASP* 6.2 3.1 - - + -
1387D SER* 5.8 9.0 - - - -
1391D GLU* 3.7 15.9 - - + -
1393D GLN* 3.2 42.7 + - + +
1394D VAL 2.8 25.8 + - - -
1395D LEU 2.8 8.6 + - - +
1397D LYS* 1.3 75.7 - - + +
1399D ASP* 1.3 61.8 - - - +
1400D VAL 3.0 2.0 - - - -
1401D GLU* 3.7 13.9 - - + +
1402D ALA* 3.0 33.8 + - - +
1415D VAL* 4.4 29.9 - - + +
1417D TRP* 5.1 17.9 - - + -
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Residues in contact with ASP1399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1395D LEU* 3.5 16.6 - - - +
1396D GLU* 2.9 45.8 + - - +
1398D TRP* 1.3 78.6 - - - +
1400D VAL* 1.3 57.0 + - - +
1402D ALA* 4.6 3.3 - - - +
1403D LEU* 2.9 36.0 + - + +
1417D TRP* 4.6 18.5 - - - -
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Residues in contact with VAL1400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197D ARG* 5.9 1.3 - - - +
1396D GLU* 3.2 28.2 + - - +
1397D LYS* 3.4 26.5 - - + +
1398D TRP 3.0 0.2 - - - -
1399D ASP* 1.3 76.6 - - - +
1401D GLU* 1.3 68.5 + - - +
1403D LEU* 3.4 8.5 + - + +
1404D ASN* 3.2 23.3 + - + +
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Residues in contact with GLU1401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385D GLY* 4.5 2.4 - - - -
1386D ASP* 4.1 28.6 + - + +
1397D LYS 3.4 9.5 + - - +
1398D TRP* 3.3 21.0 + - + +
1400D VAL* 1.3 83.9 - - - +
1402D ALA* 1.3 73.2 + - - +
1404D ASN* 3.8 2.1 - - - +
1405D GLU* 2.8 52.4 + - - +
1413D THR 4.8 0.5 - - - +
1415D VAL* 3.1 35.2 - - + +
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Residues in contact with ALA1402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1398D TRP 3.0 13.8 + - - +
1399D ASP* 4.6 3.6 - - - +
1401D GLU* 1.3 82.8 + - - +
1403D LEU* 1.3 62.6 + - - +
1405D GLU* 3.5 4.9 - - - +
1406D ARG* 3.2 29.7 + - - +
1412D LYS* 5.1 0.7 + - - +
1413D THR 5.7 0.2 - - - -
1414D PRO* 6.2 0.4 - - + -
1415D VAL* 3.3 23.3 - - + +
1417D TRP* 6.0 6.1 - - + -
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Residues in contact with LEU1403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396D GLU* 6.1 0.9 - - - +
1399D ASP* 2.9 24.0 + - + +
1400D VAL* 3.4 9.0 - - + +
1401D GLU 3.2 0.6 - - - -
1402D ALA* 1.3 78.6 - - - +
1404D ASN* 1.3 58.0 + - - +
1406D ARG* 4.9 0.7 - - - +
1407D LEU* 3.0 76.5 + - + +
1408D ILE* 5.8 2.0 - - + -
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Residues in contact with ASN1404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400D VAL* 3.2 13.5 + - + +
1401D GLU* 4.2 2.0 - - - +
1403D LEU* 1.3 77.1 - - + +
1405D GLU* 1.3 59.3 + - - +
1406D ARG 3.3 0.2 - - - -
1407D LEU* 4.0 1.6 - - - -
1408D ILE* 3.3 51.5 + - - +
1409D ALA* 2.8 35.7 + - - +
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Residues in contact with GLU1405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385D GLY* 5.5 1.7 - - - -
1401D GLU* 2.8 40.7 + - - +
1402D ALA* 3.5 7.0 - - - +
1403D LEU 3.2 0.2 - - - -
1404D ASN* 1.3 73.5 - - - +
1406D ARG* 1.3 56.6 + - + +
1409D ALA* 2.6 26.2 - - - +
1410D GLU 3.4 8.7 - - - +
1411D GLY 2.6 30.1 - - - +
1412D LYS* 4.3 1.1 - - - +
1413D THR* 3.6 40.6 + - - +
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Residues in contact with ARG1406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1402D ALA* 3.2 15.3 + - - +
1403D LEU* 5.4 0.7 - - - +
1405D GLU* 1.3 81.6 - - + +
1407D LEU* 1.3 93.4 + - + +
1409D ALA 3.9 4.7 - - - +
1410D GLU* 5.0 4.6 - - - +
1412D LYS* 2.9 57.1 - - + +
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Residues in contact with LEU1407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403D LEU* 3.0 52.4 + - + +
1406D ARG* 1.3 120.2 - - + +
1408D ILE* 1.3 81.2 + - + +
1409D ALA 4.8 1.0 - - - +
1410D GLU* 6.2 0.2 - - - +
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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