Contacts of the helix formed by residues 1400 - 1406 (chain B) in PDB entry 5IRC
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 PHE1400 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283B TYR* 3.6 39.0 - + + -
1321B MET* 4.0 23.1 - - + -
1322B LYS* 3.9 19.7 - - + -
1325B PHE* 4.6 3.6 - + - -
1375B VAL* 4.0 15.3 - - + -
1379B LEU* 4.0 25.6 - - + -
1396B LEU 3.0 13.9 + - - +
1397B SER* 3.1 1.1 + - - -
1398B ILE 3.4 1.6 + - - -
1399B CYS* 1.3 83.4 - - - +
1401B TRP* 1.3 68.2 + - - +
1402B PRO* 3.3 3.1 - - - -
1403B THR* 3.1 24.5 + - + -
1404B LEU* 3.3 35.5 + - + +
1425B ILE* 5.7 1.1 - - + -
65D ASP* 3.5 6.2 + - - -
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Residues in contact with TRP1401 (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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1397B SER* 2.8 34.6 + - - +
1400B PHE* 1.3 71.6 - - - +
1402B PRO* 1.4 76.1 - - + +
1404B LEU* 3.0 8.2 + - - +
1405B MET* 2.9 30.6 + - + +
1407B PRO* 3.5 37.0 - - + -
1409B PHE* 4.2 6.7 - + - -
1418B THR* 3.6 39.0 - - + -
1421B TYR* 3.5 31.0 - + + -
1422B GLN* 3.6 31.9 + - + +
1425B ILE* 3.6 35.6 - - + +
66D TYR* 3.6 16.0 + + - -
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Residues in contact with PRO1402 (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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1398B ILE 4.1 6.5 - - - +
1400B PHE 3.5 4.3 - - - -
1401B TRP* 1.4 117.0 - - + +
1403B THR* 1.3 56.8 + - - +
1406B ARG* 2.8 29.6 + - - +
1407B PRO* 3.6 25.1 - - + +
1409B PHE* 4.7 0.2 - - + -
65D ASP* 3.3 37.9 - - + +
66D TYR* 3.8 18.6 - - + -
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Residues in contact with THR1403 (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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1322B LYS* 3.7 30.1 - - + +
1325B PHE* 3.5 40.4 - - + +
1326B SER* 4.5 10.3 + - - +
1331B PRO* 5.5 0.5 - - - +
1332B LEU 5.2 2.4 + - - -
1400B PHE* 3.1 30.2 + - + -
1402B PRO* 1.3 80.4 - - - +
1404B LEU* 1.3 60.1 + - + +
1406B ARG* 4.6 5.5 + - - +
64D GLU* 5.6 0.9 - - - +
65D ASP* 2.6 28.4 + - - +
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Residues in contact with LEU1404 (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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1325B PHE* 4.7 6.5 - - + -
1331B PRO* 3.5 2.7 - - - +
1332B LEU* 3.4 36.4 + - + -
1333B VAL* 3.1 37.7 + - + +
1372B PHE* 3.9 23.3 - - + -
1375B VAL* 4.5 9.2 - - + -
1376B ILE* 4.3 15.0 - - + -
1379B LEU* 5.4 0.7 - - + -
1400B PHE* 3.7 39.0 - - + +
1401B TRP* 3.0 10.4 + - - +
1403B THR* 1.3 83.9 - - + +
1405B MET* 1.3 59.7 + - + +
1425B ILE* 4.4 11.7 - - + -
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Residues in contact with MET1405 (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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1331B PRO* 3.7 3.1 - - - +
1333B VAL* 4.1 22.4 - - + -
1335B TYR* 3.5 6.2 - - - -
1338B GLN* 2.8 40.9 + - + +
1341B LEU* 4.3 14.6 - - + -
1401B TRP* 2.9 27.6 + - + +
1404B LEU* 1.3 84.0 - - + +
1406B ARG* 1.3 73.0 + - - +
1407B PRO* 3.6 0.9 - - + -
1421B TYR* 3.6 39.9 - - + +
1424B ILE* 4.6 8.1 - - + -
1425B ILE* 3.7 32.5 - - + -
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Residues in contact with ARG1406 (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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1325B PHE 3.0 26.1 + - - -
1326B SER* 3.3 18.5 + - - +
1328B LEU 2.8 32.0 + - - -
1329B PRO 3.4 18.4 + - - -
1330B ASP* 3.6 13.1 + - - +
1331B PRO* 3.7 15.5 - - + +
1335B TYR* 3.3 31.8 + - - +
1402B PRO 2.8 20.5 + - - +
1403B THR 5.3 3.3 + - - +
1404B LEU 3.9 0.4 - - - -
1405B MET* 1.3 76.9 - - - +
1407B PRO* 1.3 70.3 - - - +
1408B ASP* 3.9 0.7 + - - -
68D ARG* 5.8 6.3 - - - +
104F LYS* 5.7 2.4 - - - +
108F PRO* 5.6 1.2 - - - +
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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