Contacts of the helix formed by residues 1122 - 1141 (chain A) in PDB entry 6DMY
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 MET1122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LEU* 4.6 19.7 - - - -
520A HIS* 5.3 3.4 - - + -
543A ARG 5.8 2.0 - - - +
544A THR* 5.5 11.4 - - + -
547A SER* 6.4 1.8 - - - -
1099A HIS* 3.9 33.2 - - + +
1100A VAL* 4.8 7.2 - - + -
1102A LEU* 4.4 23.3 - - + -
1103A ALA* 3.7 24.7 - - + -
1118A ALA 3.9 7.8 + - - +
1119A LEU 4.7 0.2 - - - -
1120A GLU 3.3 0.2 - - - -
1121A HIS* 1.3 96.0 - - + +
1123A PHE* 1.3 65.6 + - - +
1124A ALA 3.6 1.3 - - - -
1125A PRO* 3.4 16.5 - - - +
1126A VAL* 3.3 18.4 - - + +
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Residues in contact with PHE1123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A SER* 4.5 17.7 - - - -
736A ALA* 5.2 6.3 - - + -
737A GLU* 4.5 14.6 - - + -
740A TYR* 4.3 22.0 - + + -
1100A VAL* 6.2 1.6 - - - -
1119A LEU* 3.3 29.2 + - + +
1120A GLU 3.8 8.9 + - - +
1121A HIS 3.8 0.2 - - - -
1122A MET* 1.3 76.6 - - - +
1124A ALA* 1.3 64.9 + - + +
1125A PRO* 4.1 0.2 - - - +
1126A VAL* 3.1 8.7 + - - +
1127A LEU* 3.0 43.1 + - + +
1168A LEU* 3.7 42.5 - - + +
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Residues in contact with ALA1124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A HIS* 5.1 6.7 - - + +
733A SER* 5.6 11.4 - - - +
1123A PHE* 1.3 85.1 - - + +
1125A PRO* 1.3 61.7 - - + +
1127A LEU* 3.4 8.8 + - - +
1128A ASP* 2.9 35.8 + - - +
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Residues in contact with PRO1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ASP* 5.3 5.4 - - - +
516A PHE* 4.6 2.6 - - - +
517A LEU* 3.8 43.7 - - + +
520A HIS* 3.7 32.1 - - + +
1095A GLU* 5.2 3.3 - - - +
1099A HIS* 6.2 1.6 - - + -
1122A MET* 3.4 23.8 - - + +
1124A ALA* 1.3 92.1 - - + +
1126A VAL* 1.3 56.9 + - + -
1128A ASP* 3.4 12.6 + - + +
1129A GLY* 2.9 21.3 + - - -
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Residues in contact with VAL1126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A GLU* 5.5 2.2 - - - -
1096A PHE* 4.0 31.9 - - + +
1099A HIS* 3.9 35.2 - - + -
1100A VAL* 4.9 10.3 - - + -
1122A MET* 3.3 17.0 + - + +
1123A PHE* 3.1 8.7 + - - +
1125A PRO* 1.3 76.1 - - + +
1127A LEU* 1.3 60.1 + - - +
1129A GLY* 2.9 18.5 + - - +
1130A ALA* 3.0 11.3 + - - +
1164A VAL* 4.8 4.9 - - + +
1168A LEU* 4.0 26.0 - - + -
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Residues in contact with LEU1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A TYR* 5.1 2.5 - - - +
1123A PHE* 3.0 31.1 + - + +
1124A ALA* 3.7 11.7 - - - +
1125A PRO 3.3 0.2 - - - -
1126A VAL* 1.3 77.4 - - - +
1128A ASP* 1.3 61.3 + - - +
1130A ALA* 3.0 28.0 + - + +
1131A VAL* 3.0 29.7 + - + +
1164A VAL* 5.2 11.2 - - + -
1168A LEU* 5.0 6.4 - - + +
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Residues in contact with ASP1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A TYR* 3.5 21.1 + - - -
456A THR* 4.5 10.2 - - - +
457A MET* 6.1 0.2 - - - +
513A ASP* 3.9 2.7 - - - -
516A PHE* 3.5 39.1 - - + +
1124A ALA* 2.9 23.7 + - - +
1125A PRO* 3.4 12.0 - - - +
1126A VAL 3.2 0.2 - - - -
1127A LEU* 1.3 78.5 - - - +
1129A GLY* 1.3 51.2 + - - +
1130A ALA 3.1 0.2 - - - -
1131A VAL 4.4 1.1 - - - +
1132A SER* 2.7 41.9 + - - -
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Residues in contact with GLY1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ASP* 3.3 23.5 - - - +
1095A GLU* 4.9 4.0 - - - -
1096A PHE* 3.6 24.6 - - - -
1125A PRO 2.9 11.1 + - - -
1126A VAL* 2.9 14.5 + - - -
1128A ASP* 1.3 75.9 - - - +
1130A ALA* 1.3 56.5 + - - +
1132A SER* 4.1 2.0 - - - -
1133A THR* 4.1 13.0 + - - -
1160A THR* 5.3 1.0 - - - +
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Residues in contact with ALA1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126A VAL 3.0 5.3 + - - +
1127A LEU* 3.0 20.3 + - + +
1129A GLY* 1.3 76.4 - - - +
1131A VAL* 1.3 67.1 + - + +
1132A SER 3.2 2.1 + - - -
1133A THR* 3.5 2.1 + - - -
1134A LEU* 2.9 35.6 + - + +
1160A THR* 4.6 8.0 - - - +
1161A ILE* 6.2 3.8 - - + -
1164A VAL* 3.6 28.0 - - + -
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Residues in contact with VAL1131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A TYR* 3.4 39.9 - - + +
1127A LEU* 3.0 33.3 + - + +
1128A ASP 4.8 0.2 - - - +
1130A ALA* 1.3 78.7 - - + +
1132A SER* 1.3 53.8 + - - +
1134A LEU* 4.4 10.3 - - + -
1135A LEU* 2.6 52.4 + - + +
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Residues in contact with SER1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A MET* 4.3 23.6 - - - +
452A TYR* 4.6 4.5 - - - -
509A GLY* 3.5 12.7 + - - -
512A VAL* 4.7 5.2 - - - -
513A ASP* 2.3 31.4 + - - -
516A PHE* 4.5 12.8 - - - -
1128A ASP 2.7 17.2 + - - -
1129A GLY* 3.8 1.2 - - - -
1131A VAL* 1.3 78.3 - - - +
1133A THR* 1.3 66.8 + - - +
1135A LEU* 3.7 1.0 - - - +
1136A GLY* 3.0 26.2 + - - -
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Residues in contact with THR1133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A LEU* 5.7 1.3 - - + +
509A GLY* 2.7 31.1 + - - +
510A VAL* 4.1 11.9 + - + +
513A ASP* 3.6 11.8 + - - -
1092A ILE* 5.2 11.9 - - + +
1129A GLY 4.1 7.4 + - - -
1130A ALA 3.5 3.0 + - - -
1132A SER* 1.3 80.9 + - - +
1134A LEU* 1.3 58.8 + - - +
1136A GLY* 3.4 0.9 + - - -
1137A VAL* 3.0 43.1 + - + +
1156A LEU* 5.1 9.9 - - + -
1160A THR* 3.8 22.4 - - + -
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Residues in contact with LEU1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130A ALA* 2.9 22.4 + - + +
1131A VAL* 4.4 8.5 - - + -
1133A THR* 1.3 77.4 - - - +
1135A LEU* 1.3 52.3 + - + +
1137A VAL* 4.9 2.7 - - - -
1138A LEU* 2.7 58.6 + - + +
1153A PHE* 5.8 0.7 - - + -
1157A ALA* 3.8 31.0 - - + +
1160A THR* 3.6 25.1 - - - +
1161A ILE* 4.6 15.7 - - + -
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Residues in contact with LEU1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A LEU* 3.8 28.8 - - + +
449A MET* 4.8 9.4 - - - -
452A TYR* 3.7 40.8 - - + -
1131A VAL* 2.6 31.0 + - + +
1132A SER* 3.7 2.5 - - - +
1133A THR 3.1 0.2 - - - -
1134A LEU* 1.3 78.1 - - + +
1136A GLY* 1.3 60.7 + - - +
1138A LEU* 3.4 25.6 - - + +
1139A MET* 3.0 26.5 + - - +
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Residues in contact with GLY1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A MET* 5.0 9.5 - - - -
505A PHE* 3.8 23.9 - - - -
508A LEU* 5.9 2.7 - - - -
509A GLY* 5.2 4.3 - - - -
1132A SER 3.0 13.8 + - - -
1133A THR 3.9 1.3 - - - -
1135A LEU* 1.3 76.8 - - - +
1137A VAL* 1.3 57.4 + - - +
1139A MET* 3.1 8.7 + - - +
1140A LEU* 3.0 22.0 + - - +
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Residues in contact with VAL1137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A PHE 4.3 14.1 - - - +
506A LEU* 5.0 7.0 - - + +
509A GLY* 6.2 0.4 - - - -
1133A THR* 3.0 24.6 + - + +
1134A LEU* 4.6 3.4 - - - +
1136A GLY* 1.3 74.9 - - - +
1138A LEU* 1.3 58.4 + - - +
1140A LEU* 2.9 26.8 + - + +
1141A ALA 3.1 10.4 + - - -
1152A PHE 4.1 1.3 - - - +
1153A PHE* 3.2 33.3 - - + +
1156A LEU* 3.7 37.2 - - + -
1157A ALA* 4.2 5.8 - - + +
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Residues in contact with LEU1138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A LEU* 6.0 3.4 - - + -
1134A LEU* 2.7 45.3 + - + +
1135A LEU* 3.4 26.0 - - + +
1136A GLY 3.2 0.2 - - - -
1137A VAL* 1.3 77.6 - - - +
1139A MET* 1.3 60.8 + - + +
1141A ALA* 4.0 11.4 + - - +
1153A PHE* 4.1 14.6 - - + -
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Residues in contact with MET1139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.7 22.7 + - + +
444A SER* 4.6 6.7 - - - +
445A GLY* 3.6 33.9 - - - +
448A LEU* 3.8 33.4 - - + -
505A PHE* 3.9 14.5 - - + -
1135A LEU 3.0 11.9 + - - +
1136A GLY* 3.1 9.2 + - - +
1138A LEU* 1.3 76.3 - - + +
1140A LEU* 1.3 59.2 + - - +
1141A ALA 2.9 18.5 - - - +
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Residues in contact with LEU1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ARG* 4.1 10.3 + - - +
501A GLN* 3.3 33.7 - - + +
502A VAL* 4.3 8.1 - - + +
505A PHE* 3.7 25.3 - - + -
506A LEU 5.7 0.2 - - - +
1136A GLY 3.0 7.7 + - - +
1137A VAL* 2.9 25.1 + - + +
1139A MET* 1.3 76.6 - - - +
1141A ALA* 1.3 59.6 + - - +
1143A SER* 4.3 2.9 + - - -
1148A ILE* 3.7 34.2 - - + +
1152A PHE* 4.3 9.9 - - + -
1153A PHE* 4.1 23.8 - - + +
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Residues in contact with ALA1141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ARG* 3.3 8.5 + - - -
1137A VAL 3.1 5.7 + - - -
1138A LEU 4.2 9.4 - - - +
1139A MET* 2.9 17.0 - - - +
1140A LEU* 1.3 78.5 - - - +
1142A GLY* 1.3 61.5 + - - +
1143A SER* 3.3 1.1 - - - +
1148A ILE* 5.7 0.4 - - - -
1149A VAL* 4.8 4.9 - - + -
1153A PHE* 3.6 47.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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