Contacts of the helix formed by residues 1198 - 1211 (chain B) in PDB entry 3CQZ
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 PRO1198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1428A VAL 4.0 4.5 - - - +
1429A ILE* 3.1 27.8 - - - +
1430A LEU 3.3 13.9 - - - +
1431A GLY* 3.5 15.9 - - - +
1152B MET* 5.2 9.4 - - + -
1153B GLU* 6.3 0.7 - - + -
1155B SER* 3.6 23.8 - - - +
1156B ASP 4.7 2.2 - - - +
1157B ALA* 4.9 0.9 - - - +
1197B ILE* 1.3 87.3 - - + +
1199B TYR* 1.3 67.0 + - - +
1200B ALA* 4.5 3.4 - - + +
1201B ALA* 2.9 23.5 + - - +
1202B LYS 3.3 3.3 + - - -
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Residues in contact with TYR1199 (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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75A ASN* 6.0 3.6 - - - -
245A PRO* 3.7 15.9 + - - +
1155B SER* 3.3 22.7 + - - +
1156B ASP 4.3 0.8 + - - +
1158B PHE* 3.7 39.7 - + + -
1197B ILE 3.4 2.6 + - - -
1198B PRO* 1.3 69.6 - - - +
1200B ALA* 1.3 66.3 + - - +
1202B LYS* 2.8 42.4 + - + +
1203B LEU* 2.9 52.1 + - + +
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Residues in contact with ALA1200 (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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1155B SER* 3.8 10.0 + - - +
1198B PRO* 3.3 3.8 - - + -
1199B TYR* 1.3 78.2 - - - +
1201B ALA* 1.3 51.1 + - - +
1203B LEU* 3.3 11.1 + - - +
1204B LEU* 2.8 37.4 + - - +
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Residues in contact with ALA1201 (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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1429A ILE* 3.5 35.1 + - + +
1430A LEU* 5.0 0.2 - - - -
1197B ILE* 3.9 11.4 - - + -
1198B PRO* 2.9 20.3 + - - +
1200B ALA* 1.3 72.0 - - - +
1202B LYS* 1.3 63.7 + - - +
1204B LEU* 3.0 8.1 + - - +
1205B PHE* 2.8 48.0 + - + -
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Residues in contact with LYS1202 (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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78A PRO* 3.0 32.9 + - - -
245A PRO* 3.5 8.1 - - - +
1158B PHE* 3.6 35.6 - - + -
1160B VAL* 4.2 0.7 - - + -
1169B MET* 3.4 28.6 - - - +
1197B ILE* 3.5 18.8 - - + +
1198B PRO 3.3 2.5 + - - +
1199B TYR* 2.8 47.3 + - + +
1201B ALA* 1.3 75.6 - - - +
1203B LEU* 1.3 61.9 + - - +
1205B PHE 3.4 0.3 + - - -
1206B GLN* 3.0 55.2 + - - +
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Residues in contact with LEU1203 (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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245A PRO 3.5 26.5 - - - +
246A VAL* 4.1 14.4 - - + +
1199B TYR* 2.9 42.7 + - + +
1200B ALA* 3.4 11.9 - - - +
1202B LYS* 1.3 76.2 - - - +
1204B LEU* 1.3 52.6 + - - +
1206B GLN* 3.1 17.7 + - - +
1207B GLU* 2.7 48.9 + - - +
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Residues in contact with LEU1204 (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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1399A ARG* 3.5 27.8 - - - +
1401A SER* 5.3 7.9 - - - +
1404A GLU* 6.1 4.0 - - + -
1409A LEU* 5.4 10.8 - - + -
1429A ILE* 5.6 2.5 - - + -
1200B ALA 2.8 20.5 + - - +
1201B ALA* 3.7 4.7 - - - +
1203B LEU* 1.3 72.4 - - - +
1205B PHE* 1.3 68.7 + - + +
1207B GLU* 3.4 19.2 + - + +
1208B LEU* 3.0 42.4 + - + +
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Residues in contact with PHE1205 (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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17A VAL* 5.7 2.0 - - + -
19A PHE* 6.0 1.1 - + - -
1399A ARG* 3.4 40.8 - - - -
1429A ILE* 4.7 0.7 - - + -
1430A LEU* 3.9 20.2 - - + -
1169B MET* 3.4 20.6 - - + -
1197B ILE* 4.1 12.8 - - + -
1201B ALA* 2.8 46.3 + - + +
1202B LYS* 4.0 2.9 - - - -
1204B LEU* 1.3 78.2 - - + +
1206B GLN* 1.3 59.6 + - - +
1208B LEU* 3.3 7.3 + - + +
1209B MET* 2.9 30.8 + - - +
1215B PRO* 3.7 33.7 - - + +
1217B LEU* 4.3 22.9 - - + -
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Residues in contact with GLN1206 (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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78A PRO* 3.5 13.3 + - - +
79A GLY 4.2 5.5 + - - -
81A PHE* 3.7 19.2 - - + -
243A PRO* 4.0 17.4 - - - +
246A VAL* 3.7 19.2 - - + +
1169B MET* 3.9 12.8 - - + +
1202B LYS* 3.0 59.4 + - - +
1203B LEU* 3.1 14.5 + - - +
1205B PHE* 1.3 72.1 - - - +
1207B GLU* 1.3 58.2 + - - +
1209B MET* 3.0 9.1 + - - +
1210B ALA* 2.8 37.1 + - - +
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Residues in contact with GLU1207 (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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246A VAL* 4.3 21.6 - - + +
1203B LEU* 2.7 29.1 + - - +
1204B LEU* 3.4 27.2 + - + +
1206B GLN* 1.3 71.7 - - - +
1208B LEU* 1.3 63.0 + - - +
1210B ALA* 3.4 7.8 + - - +
1211B MET* 3.3 31.5 + - + +
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Residues in contact with LEU1208 (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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19A PHE* 4.1 18.2 - - + -
1399A ARG* 5.7 0.2 - - - +
1406A VAL* 5.7 0.2 - - + -
1409A LEU* 3.9 34.3 - - + -
1204B LEU* 3.0 36.7 + - + +
1205B PHE* 3.4 10.5 - - + +
1206B GLN 3.1 0.2 - - - -
1207B GLU* 1.3 76.8 - - + +
1209B MET* 1.3 59.3 + - - +
1211B MET* 3.2 28.6 + - + +
1213B ILE* 3.0 45.5 + - + +
1215B PRO* 4.1 26.2 - - + -
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Residues in contact with MET1209 (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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22A PHE* 3.6 33.3 - - + -
30A ILE* 4.1 12.1 - - + -
81A PHE* 3.6 38.1 - - + -
240A PRO* 3.3 12.7 - - - +
1168B LEU* 4.3 17.7 - - + -
1169B MET* 4.8 15.9 - - - +
1170B THR* 4.5 7.6 - - + -
1205B PHE 2.9 19.2 + - - +
1206B GLN* 3.0 13.7 + - - +
1208B LEU* 1.3 70.5 - - - +
1210B ALA* 1.3 55.5 + - - +
1211B MET 3.0 4.0 - - - -
1212B ASN* 2.7 24.8 + - - -
1213B ILE 3.1 6.3 - - - -
1215B PRO* 3.8 18.4 - - + -
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Residues in contact with ALA1210 (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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81A PHE* 3.9 8.5 - - + -
239A LEU* 4.2 0.5 - - - +
240A PRO* 3.9 14.1 - - - +
242A PRO* 4.0 23.8 - - + -
246A VAL* 5.3 1.6 - - + -
303A TYR* 3.7 35.9 + - + +
304A MET* 3.9 4.3 - - - +
1206B GLN 2.8 19.9 + - - +
1207B GLU* 3.6 9.2 - - - +
1208B LEU 3.3 0.2 - - - -
1209B MET* 1.3 72.1 - - - +
1211B MET* 1.3 58.3 + - + +
1212B ASN 3.3 1.8 + - - -
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Residues in contact with MET1211 (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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92A HIS* 3.1 20.8 - - + -
303A TYR* 6.1 0.2 - - + -
304A MET* 3.8 37.5 - - + +
1406A VAL* 3.8 27.1 - - + -
1409A LEU* 6.1 0.2 - - + -
1410A PHE* 4.1 20.6 - - + -
1207B GLU* 3.3 19.3 - - + +
1208B LEU* 3.2 28.6 + - + +
1209B MET 3.0 1.4 - - - -
1210B ALA* 1.3 79.5 - - + +
1212B ASN* 1.3 62.5 + - - +
1213B ILE* 3.1 13.1 + - + +
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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