Contacts of the helix formed by residues 1122 - 1135 (chain B) in PDB entry 6CNB
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 PRO1122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A LEU* 5.9 1.6 - - + -
371A LYS* 4.8 6.3 - - + +
1415A ILE 4.6 1.8 - - - +
1416A ILE 3.1 22.9 - - - +
1417A LEU 3.3 19.5 - - - +
1418A GLY* 4.0 5.2 - - - -
1083B LEU 4.1 12.1 - - - +
1084B MET* 3.4 17.9 - - - -
1088B ASP* 3.5 23.3 - - - +
1121B ILE* 1.3 88.0 - - + +
1123B TYR* 1.3 57.1 + - - +
1124B ALA* 4.3 1.3 - - + +
1125B ALA* 2.6 36.1 + - + +
1126B LYS* 3.1 5.0 + - - +
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Residues in contact with TYR1123 (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 HIS* 5.8 0.7 - - - -
267A CYS* 2.9 33.8 + - - -
268A ILE* 5.9 0.2 - - - +
1046B LEU 3.7 15.3 + - - -
1047B THR* 3.0 26.2 - - - -
1048B ARG* 3.3 43.9 + - + +
1088B ASP* 2.4 35.6 + - + +
1090B PHE* 3.5 33.4 - + + -
1121B ILE 3.3 5.4 + - - -
1122B PRO* 1.3 68.6 - - - +
1124B ALA* 1.3 54.7 + - - -
1126B LYS* 3.4 35.6 + - - +
1127B LEU* 2.9 32.3 + - + +
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Residues in contact with ALA1124 (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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363A ARG* 5.0 4.8 - - - -
367A ASN* 4.5 2.5 - - - +
368A LEU* 3.3 36.1 - - + +
371A LYS* 3.8 21.1 - - - +
1047B THR* 4.4 14.5 + - + -
1049B GLN* 4.4 4.5 - - - +
1088B ASP* 2.7 10.5 + - - +
1122B PRO* 3.1 2.9 - - + -
1123B TYR* 1.3 75.0 - - - +
1125B ALA* 1.3 55.8 + - - +
1127B LEU* 3.7 7.9 - - - +
1128B LEU* 2.9 21.3 + - - +
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Residues in contact with ALA1125 (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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368A LEU* 3.7 12.5 - - + +
1416A ILE* 4.0 27.4 - - + +
1417A LEU* 4.5 5.2 - - + -
1121B ILE* 3.8 21.8 - - + -
1122B PRO* 2.6 21.5 + - - +
1124B ALA* 1.3 72.1 - - - +
1126B LYS* 1.3 63.0 + - - +
1128B LEU* 3.0 7.1 + - - +
1129B PHE* 2.9 27.4 + - + -
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Residues in contact with LYS1126 (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 HIS* 3.7 20.1 + - + -
267A CYS* 5.6 0.4 - - - -
268A ILE* 5.1 1.4 - - - +
1090B PHE* 3.7 23.6 - - + -
1092B VAL* 3.8 16.6 - - + -
1101B MET* 3.3 32.8 - - + -
1121B ILE* 4.7 5.1 - - + +
1122B PRO 3.1 6.5 + - - +
1123B TYR* 3.4 44.7 + - - +
1125B ALA* 1.3 77.8 - - - +
1127B LEU* 1.3 61.2 + - - +
1129B PHE* 2.5 28.9 + - - +
1130B GLN* 2.6 43.2 + - - +
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Residues in contact with LEU1127 (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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267A CYS 5.0 0.7 - - - +
268A ILE* 3.4 27.8 - - + -
363A ARG* 3.1 37.5 - - - +
1046B LEU* 3.2 37.0 - - + +
1047B THR* 3.7 20.0 - - + +
1123B TYR* 2.9 26.4 + - + +
1124B ALA* 3.7 4.5 - - - +
1126B LYS* 1.3 82.5 - - - +
1128B LEU* 1.3 56.8 + - - +
1130B GLN 4.7 0.7 - - - +
1131B GLU* 2.9 40.3 + - + +
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Residues in contact with LEU1128 (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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357A LEU* 4.6 12.6 - - + -
363A ARG* 4.8 5.1 - - + +
364A PHE* 3.4 43.3 - - + -
368A LEU* 3.8 18.8 - - + -
1384A LEU* 5.1 9.6 - - + -
1396A LEU* 6.0 1.1 - - + -
1416A ILE* 5.5 5.4 - - + -
1124B ALA 2.9 14.9 + - - +
1125B ALA* 3.1 11.7 - - - +
1126B LYS 2.9 0.4 - - - -
1127B LEU* 1.3 75.0 - - - +
1129B PHE* 1.3 72.6 + - + +
1131B GLU* 3.6 8.4 - - - +
1132B LEU* 2.9 54.6 + - + +
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Residues in contact with PHE1129 (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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16A LEU* 4.2 12.8 - - + -
1384A LEU* 6.1 1.3 - - + -
1416A ILE* 6.5 0.2 - - + -
1417A LEU* 4.4 16.2 - - + -
1101B MET* 3.6 34.1 - - + -
1121B ILE* 4.4 13.9 - - + -
1125B ALA* 2.9 15.3 + - + -
1126B LYS* 2.5 18.4 + - - +
1128B LEU* 1.3 86.4 - - + +
1130B GLN* 1.3 67.6 + - - +
1132B LEU* 2.7 17.0 + - + -
1133B LEU* 2.8 18.6 + - + +
1139B PRO* 3.4 35.2 - - + -
1141B LEU* 3.8 39.9 - - + -
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Residues in contact with GLN1130 (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 HIS* 2.7 34.3 + - - +
79A GLY 4.0 10.5 + - - -
80A HIS* 5.5 0.2 - - - +
81A PHE* 4.1 28.6 - - + -
265A PRO* 4.2 9.9 - - - +
267A CYS* 5.5 0.3 - - - +
268A ILE* 3.6 28.1 - - + +
1101B MET* 3.7 22.5 - - + +
1126B LYS* 2.6 40.8 + - - +
1127B LEU 4.5 0.2 - - - +
1129B PHE* 1.3 72.6 - - - +
1131B GLU* 1.3 63.9 + - - +
1134B SER* 3.3 20.4 + - - -
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Residues in contact with GLU1131 (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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268A ILE* 4.2 21.7 - - + +
353A PHE* 3.5 19.9 - - + -
356A ARG* 3.3 25.4 + - - +
357A LEU* 3.2 31.7 - - + +
363A ARG* 2.4 43.5 + - - +
1127B LEU* 2.9 23.5 + - + +
1128B LEU* 3.6 5.6 - - - +
1129B PHE 2.9 0.6 + - - -
1130B GLN* 1.3 77.3 - - - +
1132B LEU* 1.3 71.4 + - - +
1134B SER* 3.1 13.3 + - - -
1135B MET* 3.4 2.3 + - - -
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Residues in contact with LEU1132 (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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18A PHE* 5.2 10.8 - - + -
357A LEU* 4.5 5.6 - - + +
1384A LEU* 5.9 1.8 - - + -
1396A LEU* 3.7 28.3 - - + -
1128B LEU* 2.9 41.6 + - + +
1129B PHE* 2.7 10.6 + - + +
1131B GLU* 1.3 69.0 - - - +
1133B LEU* 1.3 51.4 + - - +
1135B MET* 2.4 68.2 + - + +
1137B ILE* 3.6 22.9 - - + -
1139B PRO* 4.0 26.9 - - + -
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Residues in contact with LEU1133 (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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21A LEU* 3.4 39.7 - - + +
29A GLN* 4.0 5.8 - - - +
81A PHE* 3.4 38.3 - - + -
262A PRO* 4.0 8.5 - - - +
1100B LEU* 3.7 26.2 - - + -
1101B MET* 5.7 6.3 - - + -
1129B PHE* 2.8 20.3 + - + +
1130B GLN* 5.7 0.2 - - - -
1132B LEU* 1.3 72.5 - - - +
1134B SER* 1.3 59.7 + - - +
1135B MET 2.8 8.6 - - - +
1136B ASN* 4.5 0.5 - - - -
1137B ILE 3.1 21.0 - - - +
1138B ALA* 3.9 11.4 - - + -
1139B PRO* 4.6 5.4 - - + -
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Residues in contact with SER1134 (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* 4.9 5.0 - - - -
258A TRP* 4.5 1.4 - - - -
261A LEU* 5.1 0.7 - - - +
262A PRO* 3.0 44.8 + - - +
263A ALA 5.5 0.4 - - - -
264A PRO* 3.2 34.8 - - - +
326A TYR* 3.6 9.3 + - - -
353A PHE* 4.4 8.5 - - - -
1130B GLN 3.3 15.6 + - - -
1131B GLU* 3.1 13.6 + - - -
1132B LEU 2.8 4.0 + - - -
1133B LEU* 1.3 68.3 - - - +
1135B MET* 1.3 64.4 + - - -
1136B ASN 3.7 0.2 + - - -
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Residues in contact with MET1135 (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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258A TRP* 4.4 5.4 - - + -
326A TYR* 5.9 1.7 - - - -
327A ILE* 4.7 19.1 - - + +
353A PHE* 3.5 37.5 - - + -
354A CYS* 5.9 2.9 - - - -
357A LEU* 4.1 14.6 - - + -
1396A LEU* 5.5 2.9 - - + -
1397A PHE* 3.2 43.5 - - + -
1131B GLU 3.4 1.0 + - - -
1132B LEU* 2.4 56.7 + - + +
1133B LEU 2.8 11.1 - - - +
1134B SER* 1.3 74.9 + - - +
1136B ASN* 1.3 66.5 + - - +
1137B ILE* 3.0 11.4 + - + -
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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