Contacts of the helix formed by residues 1127 - 1138 (chain A) in PDB entry 3I7O
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 ASP1127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A PHE* 6.1 0.4 - - - -
1102A ARG* 2.7 40.9 + - - +
1125A THR* 3.7 7.4 - - - +
1126A ALA* 1.3 83.6 - - - +
1128A ASP* 1.3 62.5 + - - +
1129A LEU 2.8 10.0 - - - +
1130A ILE* 2.9 43.9 - - + +
1131A LYS* 3.7 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125A THR* 3.5 29.6 + - + +
1127A ASP* 1.3 81.7 + - - +
1129A LEU* 1.3 66.4 + - + +
1131A LYS* 3.3 24.9 - - - +
1132A VAL* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050A LEU* 3.6 33.2 - - + -
1054A MET* 3.9 20.6 - - + -
1097A PHE* 4.3 17.7 - - + -
1109A VAL* 5.4 11.0 - - + -
1124A ALA* 6.0 1.1 - - - -
1125A THR* 5.0 12.3 - - - +
1126A ALA 5.4 2.9 - - - +
1127A ASP* 2.8 3.3 - - - +
1128A ASP* 1.3 96.9 - - + +
1130A ILE* 1.3 54.2 + - - +
1131A LYS 2.8 4.7 - - - -
1132A VAL* 2.6 46.2 + - + +
1133A VAL* 2.7 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LYS* 6.0 3.1 - - - +
628A LYS 6.1 0.9 - - - +
1097A PHE* 4.1 8.2 - - + -
1098A LEU* 3.9 23.2 - - + +
1102A ARG* 4.4 15.9 - - - +
1105A MET* 3.3 36.8 - - + -
1127A ASP* 2.9 35.4 - - + +
1129A LEU* 1.3 75.9 - - - +
1131A LYS* 1.3 58.0 + - + +
1133A VAL 4.2 0.2 - - - -
1134A GLU* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127A ASP 4.3 4.0 - - - +
1128A ASP* 3.3 28.2 + - - +
1129A LEU 2.7 1.4 + - - -
1130A ILE* 1.3 81.9 - - + +
1132A VAL* 1.3 62.6 + - + +
1133A VAL 3.2 1.6 - - - -
1134A GLU* 3.5 15.0 + - - +
1135A GLU* 2.9 34.7 + - + +
1138A ARG* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A TRP* 3.5 38.0 - - + -
1050A LEU* 5.0 9.9 - - + -
1051A LEU* 5.0 6.5 - - + -
1128A ASP* 3.3 15.5 + - - +
1129A LEU* 2.6 37.7 + - + +
1131A LYS* 1.3 77.9 - - + +
1133A VAL* 1.3 68.0 + - + +
1135A GLU* 3.3 17.7 + - - +
1136A LEU* 3.4 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A MET* 3.9 16.8 - - + -
1094A ILE* 3.6 28.0 - - + +
1095A GLU* 4.3 20.7 - - + +
1097A PHE* 4.4 13.5 - - + -
1098A LEU* 3.5 37.0 - - + -
1129A LEU 2.7 19.6 + - - +
1132A VAL* 1.3 73.9 - - + +
1134A GLU* 1.3 65.3 + - - +
1136A LEU* 3.1 16.3 + - - +
1137A THR* 3.1 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LYS 4.5 2.9 - - - +
629A VAL* 3.9 12.0 - - - +
630A THR* 3.0 45.9 + - + +
1098A LEU* 4.5 14.4 - - + -
1130A ILE* 3.1 27.1 + - - +
1131A LYS* 3.5 17.9 + - - +
1133A VAL* 1.3 74.1 - - - +
1135A GLU* 1.3 54.7 - - - +
1136A LEU 2.7 14.2 + - - -
1137A THR* 2.3 32.0 + - - +
1138A ARG* 3.5 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A PRO* 3.8 31.9 - - + +
1047A TRP* 4.8 12.5 - - + -
1131A LYS* 2.9 24.8 + - + +
1132A VAL* 3.6 10.9 - - - +
1133A VAL 3.3 1.0 - - - -
1134A GLU* 1.3 74.0 - - - +
1136A LEU* 1.3 61.9 + - + +
1138A ARG* 3.8 30.9 + - - +
1139A ILE* 4.6 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.8 36.8 - - + +
1023A PRO* 5.0 8.5 - - + -
1024A THR* 4.1 15.7 - - + -
1043A LEU* 5.9 0.9 - - + -
1047A TRP* 4.9 14.1 - - + -
1051A LEU* 4.6 10.1 - - + -
1094A ILE* 4.3 11.0 - - + -
1095A GLU* 4.5 2.5 - - + +
1132A VAL* 3.4 24.9 - - + +
1133A VAL* 3.1 14.1 + - - +
1134A GLU 2.7 6.5 + - - -
1135A GLU* 1.3 73.7 - - + +
1137A THR* 1.3 52.7 + - - +
1138A ARG 2.4 17.2 + - - -
1139A ILE* 2.6 45.3 + - + +
1140A HIS* 4.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A LYS* 5.1 2.8 + - - -
1095A GLU* 3.6 39.6 + - + +
1098A LEU* 4.2 18.4 - - + -
1133A VAL 3.1 7.0 + - - +
1134A GLU* 2.3 33.3 + - - +
1136A LEU* 1.3 72.9 - - - +
1138A ARG* 1.3 63.1 + - - +
1139A ILE 3.3 0.8 + - - -
1140A HIS* 3.1 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A THR* 3.9 25.5 + - - +
631A LEU* 6.1 0.2 - - - +
655A ARG* 3.3 51.3 - - - +
670A ASN* 5.6 7.6 - - - +
1013A VAL* 4.3 12.9 - - - +
1134A GLU* 3.5 16.2 + - - +
1135A GLU* 3.9 34.0 - - - +
1136A LEU 2.4 14.3 + - - -
1137A THR* 1.3 76.5 + - - +
1139A ILE* 1.3 59.6 + - - -
1140A HIS 3.3 4.4 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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