Contacts of the helix formed by residues 1385 - 1394 (chain B) in PDB entry 5EIX
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 ASN1385 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1381B VAL* 2.8 25.1 - - - +
1382B ALA 3.1 5.8 + - - -
1384B LEU* 1.3 96.5 + - - +
1386B ILE* 1.3 63.1 + - - +
1387B ASP* 3.3 2.9 + - - -
1388B GLU* 3.4 15.9 + - + +
1389B VAL* 3.1 22.2 + - - +
1407B PHE* 3.4 29.9 - - + -
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Residues in contact with ILE1386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382B ALA 3.1 9.3 + - - +
1383B PHE* 3.6 17.0 + - + +
1384B LEU 3.8 0.4 - - - -
1385B ASN* 1.3 75.4 - - - +
1387B ASP* 1.3 57.4 + - - +
1389B VAL* 3.2 5.5 + - - +
1390B ILE* 2.9 45.4 + - + +
1425B LEU* 5.2 14.4 - - + -
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Residues in contact with ASP1387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385B ASN 3.3 0.4 - - - -
1386B ILE* 1.3 79.3 - - - +
1388B GLU* 1.3 57.4 - - - +
1390B ILE* 3.4 9.5 + - - +
1391B GLU* 2.9 28.4 + - - +
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Residues in contact with GLU1388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385B ASN* 3.4 18.0 + - + +
1386B ILE 3.4 0.4 - - - -
1387B ASP* 1.3 75.7 - - - +
1389B VAL* 1.3 60.6 + - - +
1391B GLU* 3.3 9.1 + - + +
1392B ILE* 2.9 43.0 + - + +
1406B ARG* 4.5 13.9 - - - +
1407B PHE* 4.2 24.1 - - + -
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Residues in contact with VAL1389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382B ALA* 3.9 25.4 - - + +
1385B ASN 3.1 19.3 + - - +
1386B ILE* 3.4 9.9 - - - +
1387B ASP 3.2 0.2 - - - -
1388B GLU* 1.3 76.3 - - - +
1390B ILE* 1.3 62.3 + - + +
1392B ILE* 3.0 6.2 + - - +
1393B ILE* 2.9 41.9 + - + +
1403B LEU* 4.3 12.8 - - + -
1407B PHE* 3.6 23.3 - - + -
1417B ILE* 4.0 24.5 - - + -
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Residues in contact with ILE1390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1386B ILE* 2.9 31.6 + - + +
1387B ASP* 3.8 6.7 - - - +
1389B VAL* 1.3 77.6 - - + +
1391B GLU* 1.3 58.2 + - - +
1393B ILE* 3.3 8.3 + - + +
1394B ARG* 2.9 57.4 + - + +
1422B LEU* 6.3 1.6 - - + -
1425B LEU* 4.8 17.9 - - + -
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Residues in contact with GLU1391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1387B ASP 2.9 14.7 + - - +
1388B GLU* 3.4 14.1 - - + +
1390B ILE* 1.3 75.8 - - - +
1392B ILE* 1.3 63.8 + - + +
1394B ARG* 3.1 6.3 + - - +
1395B THR* 2.9 32.2 + - - -
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Residues in contact with ILE1392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388B GLU* 2.9 31.7 + - + +
1389B VAL 3.4 7.0 - - - +
1391B GLU* 1.3 75.0 - - + +
1393B ILE* 1.3 63.2 + - - +
1395B THR* 5.0 1.6 - - - -
1396B GLU* 3.1 35.5 + - + +
1399B PRO* 3.7 5.4 - - + +
1402B ALA* 3.7 31.6 - - + +
1403B LEU* 3.7 26.9 - - + +
1406B ARG* 4.2 22.9 - - + -
1407B PHE* 4.9 2.0 - - + -
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Residues in contact with ILE1393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389B VAL* 2.9 31.6 + - + +
1390B ILE* 3.5 10.5 - - - +
1392B ILE* 1.3 76.6 - - - +
1394B ARG* 1.3 67.3 + - + +
1395B THR 3.4 1.4 + - - -
1396B GLU 3.9 10.6 - - - +
1399B PRO* 3.8 16.5 - - + +
1403B LEU* 4.0 17.7 - - + -
1417B ILE* 5.5 1.8 - - + +
1418B LEU* 3.6 33.7 - - + -
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Residues in contact with ARG1394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1390B ILE* 2.9 41.0 + - + +
1391B GLU* 3.5 4.5 - - - +
1393B ILE* 1.3 85.0 - - + +
1395B THR* 1.3 59.7 + - - +
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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