Contacts of the strand formed by residues 1392 - 1400 (chain A) in PDB entry 1FNF
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 GLU1392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1363A PRO* 3.2 25.6 - - - +
1364A GLU* 4.1 5.4 + - + +
1390A GLY 4.3 0.6 + - - -
1391A THR* 1.3 75.3 - - - +
1393A TYR* 1.3 60.1 + - - +
1394A VAL* 5.7 1.7 - - + +
1412A GLN* 3.2 36.3 + - + +
1413A GLN* 2.7 35.7 + - - +
1414A SER* 2.8 30.1 + - - +
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Residues in contact with TYR1393 (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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1343A PHE* 4.0 24.7 - + + -
1361A HIS* 4.0 18.4 - + + -
1362A HIS 3.3 18.6 - - - +
1363A PRO* 3.7 20.8 - - + +
1371A ARG* 5.6 1.1 - - - -
1387A LEU* 3.5 31.3 - - + -
1388A THR* 2.9 35.0 + - - +
1391A THR* 3.2 41.5 - - + +
1392A GLU* 1.3 75.3 + - - +
1394A VAL* 1.3 63.1 + - - +
1395A VAL* 3.8 5.8 + - + +
1412A GLN* 2.9 6.1 - - - -
1413A GLN 2.7 45.1 + - - +
1415A THR* 4.0 3.8 - - + -
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Residues in contact with VAL1394 (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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1360A ARG 3.6 0.9 - - - +
1361A HIS* 3.1 5.4 - - - -
1362A HIS* 2.8 64.3 + - + +
1363A PRO 5.6 2.5 - - - -
1364A GLU* 5.9 1.8 - - - +
1392A GLU* 5.7 2.2 - - + +
1393A TYR* 1.3 72.5 - - - +
1395A VAL* 1.3 61.1 + - - +
1396A SER* 5.3 1.8 - - - +
1410A ILE* 3.7 30.7 - - + -
1411A GLY 3.4 7.2 - - - +
1412A GLN* 3.7 24.2 - - + +
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Residues in contact with VAL1395 (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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1333A ILE* 3.8 8.6 - - + +
1335A PHE* 3.7 28.9 - - + -
1343A PHE* 4.0 20.6 - - + -
1345A VAL* 3.9 22.4 - - + -
1359A ILE* 3.7 26.2 - - + -
1360A ARG 3.3 4.9 - - - +
1361A HIS* 4.2 11.0 - - + -
1384A LEU* 4.5 1.3 - - + -
1393A TYR 4.3 6.1 - - - +
1394A VAL* 1.3 77.7 - - - +
1396A SER* 1.3 62.7 + - - +
1397A ILE* 4.5 1.8 - - + -
1409A LEU 3.8 0.5 - - - +
1410A ILE* 3.4 4.9 - - - +
1411A GLY 2.8 34.0 + - - +
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Residues in contact with SER1396 (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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1358A ARG 3.6 1.5 - - - +
1359A ILE* 3.2 4.5 - - - +
1360A ARG* 2.7 66.3 + - - +
1394A VAL* 4.2 1.8 - - - -
1395A VAL* 1.3 74.3 - - - +
1397A ILE* 1.3 62.9 + - - +
1408A LEU* 3.8 26.6 - - - +
1409A LEU 3.4 6.7 - - - -
1410A ILE* 4.4 12.6 - - - -
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Residues in contact with ILE1397 (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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1330A PRO* 4.1 8.1 - - + +
1333A ILE* 4.0 26.9 - - + -
1345A VAL* 4.0 6.3 - - + -
1347A TRP* 3.5 42.8 - - + -
1357A TYR* 4.0 32.5 - - + -
1358A ARG 3.4 4.5 - - - +
1359A ILE* 4.1 18.8 - - + -
1395A VAL* 4.5 1.8 - - + -
1396A SER* 1.3 82.2 - - - +
1398A VAL* 1.3 68.1 + - - +
1407A PRO 4.1 0.7 - - - +
1408A LEU* 3.7 0.3 - - - -
1409A LEU* 2.9 42.9 + - + +
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Residues in contact with VAL1398 (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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1330A PRO* 4.5 0.2 - - - -
1357A TYR* 3.2 8.8 - - - +
1358A ARG* 3.0 69.2 + - + +
1396A SER 5.5 0.2 - - - -
1397A ILE* 1.3 73.9 - - - +
1399A ALA* 1.3 61.3 + - - +
1400A LEU* 3.5 17.3 - - + -
1405A GLU* 4.1 5.4 - - - +
1406A SER* 3.8 24.7 - - - +
1407A PRO 4.2 0.2 - - - -
1408A LEU* 3.1 36.1 - - + -
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Residues in contact with ALA1399 (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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1327A LEU* 3.7 2.4 - - + +
1328A ASP 4.3 0.2 - - - +
1330A PRO* 4.0 12.7 - - + +
1350A PRO* 3.9 17.9 - - + -
1354A ILE* 3.7 21.8 - - + -
1356A GLY 3.6 6.1 - - - +
1357A TYR* 3.8 8.5 - - + -
1398A VAL* 1.3 75.2 - - - +
1400A LEU* 1.3 61.3 + - - +
1405A GLU* 3.4 2.8 - - - -
1406A SER* 2.9 44.4 + - - +
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Residues in contact with LEU1400 (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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1327A LEU* 3.8 2.9 - - - -
1354A ILE* 3.1 6.9 - - - +
1355A THR* 2.8 27.8 + - - +
1356A GLY* 3.0 11.7 + - - +
1357A TYR* 3.6 6.3 - - - +
1358A ARG* 3.6 32.5 - - + +
1374A ARG* 3.6 31.2 - - - +
1398A VAL* 3.5 15.9 - - + +
1399A ALA* 1.3 76.3 - - - +
1401A ASN* 1.3 60.6 + - - +
1402A GLY 4.5 7.9 - - - +
1404A GLU 3.1 6.1 - - - +
1405A GLU* 3.4 44.2 - - + +
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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