Contacts of the helix formed by residues 1392 - 1406 (chain D) in PDB entry 3FK2
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 THR1392 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1383D SER* 4.3 2.0 - - - -
1386D ASN* 3.7 32.5 - - + +
1390D LEU 3.4 5.5 + - - +
1391D MET* 1.3 77.0 - - - +
1393D SER* 1.3 65.9 + - - +
1394D GLU* 3.9 11.4 + - - +
1395D ASN* 3.1 26.4 + - - +
1396D LEU* 2.9 20.4 + - - +
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Residues in contact with SER1393 (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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1383D SER* 4.0 14.6 + - - -
1392D THR* 1.3 73.8 - - - +
1394D GLU* 1.3 63.2 + - - +
1396D LEU* 3.3 3.5 + - - +
1397D SER* 3.0 24.8 + - - -
1426D GLU* 4.2 9.6 + - - +
1429D ILE* 3.4 35.2 - - - +
1430D GLN* 3.9 31.7 + - - +
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Residues in contact with GLU1394 (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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1392D THR* 3.1 10.7 + - - +
1393D SER* 1.3 77.8 + - - +
1395D ASN* 1.3 68.5 + - - +
1397D SER* 2.7 18.6 + - - -
1398D ILE* 3.2 20.9 + - + +
1422D GLN* 3.6 21.8 + - - +
1426D GLU* 3.5 36.2 + - - +
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Residues in contact with ASN1395 (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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1284D ARG* 4.4 11.8 - - - +
1390D LEU 2.9 26.1 + - - -
1391D MET* 3.7 20.7 - - + +
1392D THR* 3.1 24.7 + - - +
1394D GLU* 1.3 85.4 - - - +
1396D LEU* 1.3 63.8 + - - +
1398D ILE* 3.0 29.2 + - - +
1399D CYS* 3.2 15.6 + - - -
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Residues in contact with LEU1396 (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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1282D ILE 4.4 0.4 - - - +
1283D TYR* 4.0 30.1 - - + -
1379D LEU* 3.3 38.1 - - + +
1382D VAL* 4.0 9.0 - - + -
1383D SER* 3.8 15.0 - - - +
1391D MET* 3.6 41.5 - - + +
1392D THR 2.9 13.2 + - - +
1393D SER* 3.8 4.9 - - - +
1394D GLU 3.2 0.2 - - - -
1395D ASN* 1.3 77.0 - - - +
1397D SER* 1.3 61.8 + - - +
1399D CYS* 3.2 4.5 + - - +
1400D PHE* 3.1 28.5 + - + +
1429D ILE* 3.9 14.4 - - + -
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Residues in contact with SER1397 (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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1393D SER 3.0 10.7 + - - -
1394D GLU* 2.7 20.1 + - - -
1396D LEU* 1.3 71.5 - - - +
1398D ILE* 1.3 62.7 + - - +
1400D PHE* 4.2 0.7 - - - +
1401D TRP* 2.8 35.9 + - - -
1422D GLN* 3.3 30.7 + - - +
1425D ILE* 3.6 20.9 - - - -
1426D GLU* 3.5 21.3 - - - +
1429D ILE* 3.9 1.6 - - - +
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Residues in contact with ILE1398 (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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1284D ARG* 6.5 0.7 - - + -
1394D GLU* 3.2 20.0 + - + +
1395D ASN* 3.0 26.6 + - - +
1397D SER* 1.3 78.2 - - - +
1399D CYS* 1.3 60.8 + - - +
1400D PHE 3.5 0.2 + - - -
1401D TRP* 4.0 10.5 + - - +
1402D PRO* 3.8 14.6 - - - +
1422D GLN* 3.7 33.2 - - - +
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Residues in contact with CYS1399 (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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1283D TYR* 3.6 18.4 - - + +
1284D ARG* 3.5 26.0 - - - -
1322D LYS* 3.3 26.1 + - - +
1391D MET* 3.5 25.1 - - - -
1395D ASN 3.4 14.6 - - - -
1396D LEU* 3.2 7.4 + - - +
1397D SER 3.2 0.4 - - - -
1398D ILE* 1.3 79.1 - - - +
1400D PHE* 1.3 69.1 + - + +
1402D PRO* 4.4 3.6 - - - +
1403D THR* 3.7 5.2 + - - -
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Residues in contact with PHE1400 (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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1283D TYR* 3.6 37.2 - + + -
1321D MET* 4.4 11.4 - - + -
1322D LYS* 3.5 32.1 - - + -
1325D PHE* 5.3 1.8 - + - -
1375D VAL* 4.5 12.6 - - + -
1379D LEU* 3.4 39.5 - - + -
1396D LEU* 3.1 22.1 + - + +
1397D SER* 2.9 4.4 + - - +
1399D CYS* 1.3 83.0 - - + +
1401D TRP* 1.3 67.9 + - - +
1402D PRO* 3.3 3.6 - - - -
1403D THR* 2.9 8.4 + - + -
1404D LEU* 2.8 55.3 + - + +
1425D ILE* 4.8 2.2 - - + -
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Residues in contact with TRP1401 (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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1397D SER* 2.8 33.5 + - - +
1398D ILE* 4.0 9.3 + - - +
1400D PHE* 1.3 71.4 - - - +
1402D PRO* 1.3 100.1 - - + +
1404D LEU* 4.5 2.5 - - - +
1405D MET* 3.0 28.9 + - - +
1407D PRO* 3.3 33.2 - - + -
1409D PHE* 3.9 23.6 - + - -
1418D THR* 3.8 35.9 + - + +
1421D TYR* 3.6 24.2 - + + +
1422D GLN* 3.4 32.2 + - + +
1425D ILE* 3.6 30.2 - - + +
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Residues in contact with PRO1402 (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 ILE 3.8 13.5 - - - +
1399D CYS 4.4 2.7 - - - +
1400D PHE 3.4 4.7 - - - +
1401D TRP* 1.3 136.9 - - + +
1403D THR* 1.3 59.1 + - - +
1406D ARG* 2.8 31.7 + - - +
1407D PRO* 4.2 4.5 - - + -
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Residues in contact with THR1403 (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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1322D LYS* 3.5 54.7 + - + +
1325D PHE* 3.8 26.8 - - + +
1326D SER* 3.9 15.8 - - - +
1331D PRO* 5.0 2.6 - - - +
1332D LEU 5.1 0.2 + - - -
1399D CYS 3.7 6.2 + - - -
1400D PHE* 2.9 12.0 + - + -
1402D PRO* 1.3 81.6 - - - +
1404D LEU* 1.3 63.9 + - + +
1405D MET 3.4 0.3 + - - -
1406D ARG* 4.4 11.9 + - - +
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Residues in contact with LEU1404 (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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1325D PHE* 4.3 19.5 - - + -
1331D PRO* 3.6 2.6 - - - +
1332D LEU* 3.4 35.5 + - + -
1333D VAL* 3.1 39.1 + - + +
1372D PHE* 4.1 21.3 - - + -
1375D VAL* 4.6 9.6 - - + -
1376D ILE* 4.5 11.4 - - + -
1379D LEU* 5.2 0.7 - - + -
1400D PHE* 2.8 46.9 + - + +
1401D TRP* 4.4 2.7 - - - +
1403D THR* 1.3 78.1 - - + +
1405D MET* 1.3 61.5 + - + +
1425D ILE* 4.7 9.0 - - + -
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Residues in contact with MET1405 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1331D PRO* 3.6 3.9 - - - +
1333D VAL* 3.8 15.5 - - + -
1335D TYR* 3.3 4.0 - - - -
1338D GLN* 2.6 38.6 + - + +
1341D LEU* 3.7 30.7 - - + -
1372D PHE* 5.5 0.9 - - + -
1401D TRP 3.0 14.2 + - - +
1404D LEU* 1.3 87.7 - - + +
1406D ARG* 1.3 73.6 + - - +
1407D PRO* 3.4 7.8 - - + -
1421D TYR* 3.5 33.2 - - + -
1424D ILE* 4.4 8.7 - - + -
1425D ILE* 3.6 34.1 - - + -
1428D PHE* 5.5 0.2 - - + -
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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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1325D PHE 3.7 12.5 + - - -
1326D SER* 3.3 28.7 + - - +
1328D LEU* 2.5 27.3 + - - +
1329D PRO 3.3 9.7 + - - -
1330D ASP 3.1 3.8 - - - -
1331D PRO* 3.0 32.9 - - + +
1335D TYR* 2.7 31.4 + - - +
1402D PRO 2.8 24.3 + - - +
1403D THR 4.5 5.8 + - - +
1405D MET* 1.3 73.6 - - - +
1407D PRO* 1.3 73.8 - - - +
1408D ASP* 3.4 1.0 + - - +
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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