Contacts of the helix formed by residues 1355 - 1371 (chain D) in PDB entry 6AH0
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 GLY1355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1332D GLN* 6.1 1.2 - - - -
1353D GLY* 3.5 3.0 - - - +
1354D SER* 1.3 78.5 - - - +
1356D LYS* 1.3 65.2 + - - +
1357D THR 3.1 5.0 + - - -
1358D ILE* 3.3 11.5 + - - -
1359D CYS 3.7 5.2 + - - -
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Residues in contact with LYS1356 (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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1354D SER 3.5 3.0 - - - -
1355D GLY* 1.3 73.9 - - - +
1357D THR* 1.3 65.3 + - - +
1358D ILE 3.2 0.2 - - - -
1359D CYS* 2.9 15.0 + - - +
1360D ALA 2.9 10.7 + - - -
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Residues in contact with THR1357 (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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1355D GLY* 3.1 2.8 - - - -
1356D LYS* 1.3 75.7 - - - +
1358D ILE* 1.3 57.7 + - - +
1360D ALA* 3.0 6.5 + - - +
1361D GLU* 2.9 20.6 + - - -
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Residues in contact with ILE1358 (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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1355D GLY 3.3 7.6 + - - -
1356D LYS 3.2 0.4 - - - -
1357D THR* 1.3 72.9 - - - +
1359D CYS* 1.3 60.3 + - - +
1361D GLU* 3.5 6.1 - - - +
1362D PHE* 2.9 24.6 + - - -
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Residues in contact with CYS1359 (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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1332D GLN* 6.1 4.9 - - - +
1339D VAL* 5.8 3.6 - - - -
1355D GLY 3.7 4.6 + - - -
1356D LYS* 2.9 14.0 + - - +
1358D ILE* 1.3 77.4 - - - +
1360D ALA* 1.3 60.8 + - - +
1362D PHE* 3.2 10.1 + - - +
1363D ALA* 3.6 6.9 + - - -
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Residues in contact with ALA1360 (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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1356D LYS 2.9 10.9 + - - -
1357D THR* 3.0 5.1 + - - +
1359D CYS* 1.3 75.3 - - - +
1361D GLU* 1.3 62.5 + - - +
1363D ALA* 3.0 5.6 + - - +
1364D ILE* 3.0 18.4 + - - -
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Residues in contact with GLU1361 (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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1357D THR 2.9 13.0 + - - -
1358D ILE* 3.2 8.4 + - - +
1360D ALA* 1.3 78.2 - - - +
1362D PHE* 1.3 54.8 + - - +
1364D ILE* 3.3 3.4 + - - +
1365D LEU* 2.9 25.5 + - - -
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Residues in contact with PHE1362 (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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1339D VAL 4.5 6.1 - - - +
1340D TYR* 4.7 8.5 - - - +
1358D ILE 2.9 14.0 + - - -
1359D CYS 3.2 5.1 + - - -
1360D ALA 3.1 0.8 - - - -
1361D GLU* 1.3 75.7 - - - +
1363D ALA* 1.3 56.0 + - - +
1365D LEU* 3.0 4.0 + - - +
1366D ARG* 2.9 25.1 + - - -
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Residues in contact with ALA1363 (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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1339D VAL 3.9 18.5 + - - -
1359D CYS 3.6 6.6 + - - -
1360D ALA 3.0 7.1 + - - -
1362D PHE* 1.3 75.0 - - - +
1364D ILE* 1.3 56.9 + - - +
1366D ARG* 3.3 2.3 + - - +
1367D MET* 3.0 25.1 + - - -
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Residues in contact with ILE1364 (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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1360D ALA 3.0 12.5 + - - -
1361D GLU* 3.3 5.8 + - - +
1362D PHE 3.1 0.2 - - - -
1363D ALA* 1.3 77.2 - - - +
1365D LEU* 1.3 55.1 + - - +
1367D MET* 3.3 3.5 + - - +
1368D LEU* 2.9 24.3 + - - -
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Residues in contact with LEU1365 (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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1361D GLU 2.9 14.8 + - - -
1362D PHE* 3.0 3.8 + - - +
1364D ILE* 1.3 73.0 - - - +
1366D ARG* 1.3 65.6 + - - +
1368D LEU* 3.0 4.3 + - - +
1369D LEU* 2.9 18.7 + - - -
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Residues in contact with ARG1366 (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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1339D VAL 5.9 0.4 - - - -
1340D TYR* 4.7 13.9 - - - +
1362D PHE 2.9 13.3 + - - -
1363D ALA* 3.3 4.4 + - - +
1365D LEU* 1.3 73.8 - - - +
1367D MET* 1.3 61.6 + - - +
1369D LEU* 3.0 5.6 + - - +
1370D GLN* 2.9 18.4 + - - -
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Residues in contact with MET1367 (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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1363D ALA 3.0 14.6 + - - -
1364D ILE* 3.7 4.3 - - - +
1366D ARG* 1.3 74.2 - - - +
1368D LEU* 1.3 62.1 + - - +
1370D GLN* 3.0 12.8 + - - +
1371D SER 3.1 13.9 + - - +
1374D GLY* 4.9 8.4 - - - -
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Residues in contact with LEU1368 (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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1364D ILE 2.9 14.3 + - - -
1365D LEU* 3.0 6.2 + - - +
1367D MET* 1.3 75.8 - - - +
1369D LEU* 1.3 62.1 + - - +
1371D SER 3.0 22.2 + - - +
1372D SER* 5.0 0.5 - - - -
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Residues in contact with LEU1369 (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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1365D LEU 2.9 13.6 + - - -
1366D ARG* 3.0 4.2 + - - +
1368D LEU* 1.3 74.5 - - - +
1370D GLN* 1.3 62.7 + - - +
1371D SER* 3.4 1.2 + - - -
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Residues in contact with GLN1370 (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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1366D ARG 2.9 12.7 + - - -
1367D MET* 3.0 7.3 + - - +
1369D LEU* 1.3 79.2 - - - +
1371D SER* 1.3 56.3 + - - +
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Residues in contact with SER1371 (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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1367D MET 3.1 9.0 + - - +
1368D LEU* 3.0 17.8 - - - +
1369D LEU 3.4 1.7 - - - -
1370D GLN* 1.3 79.2 - - - +
1372D SER* 1.3 68.4 + - - +
1373D GLU 3.4 2.7 - - - +
1374D GLY* 3.4 14.6 + - - +
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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