Contacts of the helix formed by residues 1441 - 1460 (chain A) in PDB entry 1NF1
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 ARG1441 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1433A LEU* 5.6 1.4 - - - +
1434A PHE* 2.7 34.8 + - - +
1435A THR* 2.9 39.2 + - - +
1437A GLU 3.9 5.1 + - - -
1438A GLU* 3.4 35.2 + - + +
1440A MET* 1.3 76.2 - - - +
1442A PRO* 1.4 67.4 - - + +
1444A ASN* 3.2 29.3 + - - +
1445A ASP* 5.3 1.0 - - - +
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Residues in contact with PRO1442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1438A GLU 4.6 1.8 - - - +
1439A HIS 3.3 21.8 - - - +
1440A MET* 3.2 2.9 - - - -
1441A ARG* 1.4 96.8 - - + +
1443A PHE* 1.3 77.3 + - + +
1444A ASN 3.1 1.4 + - - -
1445A ASP* 3.8 16.6 + - - +
1446A PHE 5.1 0.2 + - - -
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Residues in contact with PHE1443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335A ASN 5.2 2.0 - - - -
1336A GLN* 4.1 19.5 - - + -
1339A LEU* 3.7 24.5 - - + -
1340A LEU* 3.3 44.0 - - + -
1424A ILE* 4.0 21.3 - - + -
1434A PHE* 5.0 3.4 - - + -
1439A HIS 4.4 9.0 - - - -
1440A MET* 3.2 50.9 + - + +
1442A PRO* 1.3 84.4 - - + +
1444A ASN* 1.3 52.2 + - - +
1445A ASP 2.7 17.0 + - - -
1446A PHE* 2.8 17.8 + - + +
1447A VAL* 2.9 15.2 + - - +
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Residues in contact with ASN1444 (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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1432A VAL 5.0 0.2 + - - -
1433A LEU* 3.3 33.2 - - + +
1434A PHE* 2.8 63.6 + - - +
1440A MET 3.9 1.2 + - - -
1441A ARG* 3.2 25.6 + - - +
1442A PRO 3.1 1.2 - - - -
1443A PHE* 1.3 76.0 - - - +
1445A ASP* 1.3 62.8 + - - +
1447A VAL* 4.1 8.9 - - - +
1448A LYS* 2.9 26.3 + - - +
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Residues in contact with ASP1445 (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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1441A ARG 5.3 0.7 - - - +
1442A PRO* 3.8 13.3 - - - +
1443A PHE 2.9 1.2 - - - -
1444A ASN* 1.3 85.8 - - - +
1446A PHE* 1.3 62.6 + - - +
1447A VAL 3.3 0.7 - - - -
1448A LYS* 3.9 16.0 - - + +
1449A SER* 3.4 23.4 + - - -
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Residues in contact with PHE1446 (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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1340A LEU* 3.8 31.6 - - + -
1343A THR* 6.2 1.3 - - + -
1424A ILE* 5.5 3.8 - - + -
1428A ILE* 5.6 0.9 - - - -
1442A PRO 5.1 0.4 + - - -
1443A PHE* 2.8 11.5 + - + +
1445A ASP* 1.3 75.9 - - - +
1447A VAL* 1.3 67.4 + - + +
1449A SER* 2.8 23.0 + - - -
1450A ASN* 3.2 13.1 + - - +
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Residues in contact with VAL1447 (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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1424A ILE* 3.7 28.0 - - + +
1427A SER* 4.0 23.8 - - - +
1428A ILE* 3.9 30.8 - - + +
1431A HIS* 6.4 0.2 - - - -
1432A VAL 4.5 3.4 - - - +
1433A LEU* 4.4 15.0 - - + -
1434A PHE* 4.4 8.3 - - + -
1443A PHE 2.9 20.2 + - - +
1444A ASN* 4.3 8.3 - - - +
1446A PHE* 1.3 78.3 - - - +
1448A LYS* 1.3 61.6 + - - +
1449A SER 3.1 2.1 + - - -
1450A ASN* 3.0 15.8 + - - +
1451A PHE* 3.8 8.3 + - + +
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Residues in contact with LYS1448 (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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1433A LEU* 3.8 30.9 - - + +
1444A ASN 2.9 23.8 - - - +
1445A ASP* 3.9 18.2 - - + +
1447A VAL* 1.3 79.8 - - - +
1449A SER* 1.3 62.1 + - - +
1450A ASN 3.3 0.4 + - - -
1451A PHE* 4.1 15.8 + - - +
1452A ASP 5.5 0.2 + - - -
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Residues in contact with SER1449 (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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1445A ASP 3.4 15.6 + - - -
1446A PHE* 2.8 23.1 + - - -
1447A VAL 3.1 0.2 + - - -
1448A LYS* 1.3 77.7 - - - +
1450A ASN* 1.3 66.1 + - - +
1451A PHE 3.8 0.2 - - - -
1452A ASP* 5.4 2.0 + - - +
1453A ALA* 5.3 0.7 - - - +
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Residues in contact with ASN1450 (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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1344A GLU* 5.4 9.9 - - - +
1347A PHE* 3.7 27.6 - - + -
1428A ILE* 3.7 17.4 - - - +
1446A PHE* 3.2 13.6 + - - +
1447A VAL 3.0 14.9 - - - +
1449A SER* 1.3 84.8 + - - +
1451A PHE* 1.3 57.4 + - - +
1452A ASP 3.5 1.3 - - - +
1453A ALA* 3.7 21.7 - - + +
1454A ALA* 3.2 24.8 + - - +
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Residues in contact with PHE1451 (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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1428A ILE* 4.6 7.6 - - - +
1431A HIS* 3.8 27.5 - - + +
1447A VAL* 3.8 8.1 + - + +
1448A LYS* 4.1 14.5 + - - +
1449A SER 3.8 1.4 - - - -
1450A ASN* 1.3 76.8 - - - +
1452A ASP* 1.3 67.0 + - - +
1453A ALA 3.3 0.4 - - - -
1454A ALA* 3.6 4.8 + - - +
1455A ARG* 3.4 27.5 + - - +
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Residues in contact with ASP1452 (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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1448A LYS 5.5 0.2 + - - -
1449A SER 5.4 0.2 + - - -
1450A ASN* 4.3 0.2 - - - +
1451A PHE* 1.3 78.5 - - - +
1453A ALA* 1.3 62.9 + - - +
1454A ALA 3.3 0.4 - - - -
1455A ARG* 3.1 35.4 + - - +
1456A ARG* 3.4 39.5 + - - +
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Residues in contact with ALA1453 (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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1347A PHE* 5.0 4.7 - - + -
1351A ILE* 4.2 18.0 - - + +
1449A SER 5.3 1.1 + - - +
1450A ASN* 3.7 27.4 + - + +
1451A PHE 3.3 0.2 - - - -
1452A ASP* 1.3 81.5 - - - +
1454A ALA* 1.3 59.3 + - - +
1455A ARG 3.7 0.3 + - - -
1456A ARG* 3.5 40.6 + - - +
1457A PHE* 3.9 5.0 + - - +
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Residues in contact with ALA1454 (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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1347A PHE* 3.6 22.2 - - + -
1351A ILE* 4.3 5.2 - - - -
1428A ILE* 3.7 16.6 - - + +
1431A HIS* 5.8 0.9 - - + -
1450A ASN 3.2 17.6 + - - +
1451A PHE* 3.9 5.2 - - - +
1452A ASP 3.3 0.4 - - - -
1453A ALA* 1.3 76.9 - - - +
1455A ARG* 1.3 60.8 + - - +
1456A ARG 3.4 0.2 - - - -
1457A PHE* 3.8 2.8 + - - +
1458A PHE* 3.0 47.6 + - + -
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Residues in contact with ARG1455 (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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1379A ASN* 6.2 2.2 - - - +
1381A ILE* 3.4 28.2 - - + +
1382A GLY* 6.4 0.9 - - - -
1431A HIS* 3.8 23.8 - - + +
1451A PHE* 3.4 16.9 + - - +
1452A ASP* 3.1 46.1 + - - +
1453A ALA 3.4 0.2 - - - -
1454A ALA* 1.3 77.1 - - - +
1456A ARG* 1.3 56.0 + - - +
1458A PHE* 3.2 3.3 + - + -
1459A LEU* 2.8 45.6 + - + +
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Residues in contact with ARG1456 (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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1452A ASP* 3.4 19.4 + - - +
1453A ALA* 3.5 45.6 + - - +
1454A ALA 3.4 0.4 - - - -
1455A ARG* 1.3 78.8 - - - +
1457A PHE* 1.3 52.5 + - - +
1459A LEU* 3.2 8.2 + - - +
1460A ASP* 2.8 44.6 + - - +
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Residues in contact with PHE1457 (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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1296A TYR* 4.1 14.6 - - - -
1350A ILE* 3.4 37.5 - - + -
1351A ILE* 3.7 44.0 - - + +
1354A SER* 3.7 22.0 - - - -
1357A PHE* 5.5 1.3 - + - -
1388A MET* 3.7 20.6 - - + -
1389A PHE* 5.0 0.2 - + - -
1393A ILE* 5.6 1.1 - - + -
1453A ALA 3.9 2.2 + - - +
1454A ALA 3.8 2.6 + - - +
1455A ARG 3.3 0.4 - - - -
1456A ARG* 1.3 75.2 - - - +
1458A PHE* 1.3 88.7 + + - +
1459A LEU 3.1 1.3 - - - -
1460A ASP* 3.7 7.6 - - - +
1461A ILE* 3.0 54.9 + - + +
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Residues in contact with PHE1458 (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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1381A ILE* 3.5 28.8 - - + +
1382A GLY* 5.4 2.9 - - - -
1384A VAL* 5.1 5.4 - - + +
1385A GLY* 3.6 32.8 - - - +
1388A MET* 3.8 17.5 - - + -
1389A PHE* 3.9 25.4 - + - -
1429A ALA* 4.6 15.9 - - + -
1431A HIS* 5.7 3.8 - + - -
1454A ALA* 3.0 34.5 + - + -
1455A ARG* 3.2 10.2 + - + +
1457A PHE* 1.3 104.7 - + - +
1459A LEU* 1.3 61.2 + - - +
1461A ILE* 3.4 9.7 - - + +
1462A ALA* 3.3 25.3 + - - +
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Residues in contact with LEU1459 (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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1369A TYR* 4.1 19.3 - - + +
1381A ILE* 3.7 37.9 - - + -
1455A ARG* 2.8 24.6 + - + +
1456A ARG* 3.4 8.5 - - - +
1458A PHE* 1.3 76.8 - - - +
1460A ASP* 1.3 64.9 + - - +
1462A ALA* 3.6 5.4 + - - +
1463A SER* 3.4 27.9 + - - +
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Residues in contact with ASP1460 (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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1354A SER* 4.3 18.9 + - - +
1362A ARG* 2.8 25.3 + - - +
1456A ARG* 2.8 28.6 + - - +
1457A PHE* 3.7 8.4 - - - +
1459A LEU* 1.3 78.3 - - - +
1461A ILE* 1.3 52.5 + - - +
1462A ALA 3.2 4.7 + - - -
1463A SER* 3.3 14.5 + - - -
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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
------------------------------------------------------------
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