Contacts of the helix formed by residues 1116 - 1126 (chain G) in PDB entry 6C3P
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 PRO1116 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824G GLU 3.3 22.2 - - - +
825G ARG* 3.8 19.7 - - - +
826G GLY 4.5 6.7 - - - +
1114G THR 3.7 6.1 - - - +
1115G THR* 1.3 104.4 - - + +
1117G LEU* 1.3 65.9 + - - +
1118G GLY* 3.3 2.1 + - - +
1119G SER* 3.4 20.0 + - - +
1120G ILE 3.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503G LEU* 3.5 39.9 - - + +
504G ARG* 4.4 29.4 - - - +
506G ILE* 5.2 2.2 - - + -
824G GLU 4.5 2.4 + - - -
1112G PHE* 4.7 26.7 - - + +
1115G THR 4.9 2.0 - - - +
1116G PRO* 1.3 71.1 - - - +
1118G GLY* 1.3 65.9 + - - +
1119G SER 3.2 0.2 + - - -
1120G ILE* 3.3 13.7 - - + +
1121G LEU* 2.9 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824G GLU* 4.8 8.0 + - - +
1116G PRO* 3.3 2.8 - - - +
1117G LEU* 1.3 77.9 - - - +
1119G SER* 1.3 61.7 + - - +
1121G LEU* 3.4 11.4 + - - +
1122G ASN* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115G THR* 4.9 6.5 - - - -
1116G PRO* 3.4 20.4 + - - +
1117G LEU 3.2 0.8 - - - -
1118G GLY* 1.3 73.9 - - - +
1120G ILE* 1.3 56.5 + - - +
1122G ASN* 2.8 27.4 + - - +
1123G ARG* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503G LEU* 4.7 11.0 - - + -
1100G LEU* 6.0 0.7 - - + -
1104G ILE* 3.7 41.1 - - + -
1111G PHE* 3.9 26.5 - - + -
1112G PHE* 5.8 4.7 - - + -
1115G THR* 4.3 14.1 - - + +
1116G PRO 3.7 9.7 + - - +
1117G LEU* 3.3 25.4 - - + +
1119G SER* 1.3 76.9 - - - +
1121G LEU* 1.3 62.6 + - - +
1123G ARG* 3.8 12.3 + - + +
1124G PHE* 3.7 16.9 - - + -
1317G LEU* 4.2 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499G THR* 3.9 29.6 - - + +
500G ASN* 3.1 34.3 - - - +
503G LEU* 4.9 10.5 - - + -
504G ARG* 3.9 24.7 - - - +
1117G LEU* 2.9 20.9 + - + +
1118G GLY* 3.6 10.3 - - - +
1120G ILE* 1.3 75.5 - - + +
1122G ASN* 1.3 65.6 + - - +
1123G ARG 3.1 3.7 + - - -
1124G PHE* 3.1 7.7 + - + +
1125G SER* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118G GLY 2.9 13.4 + - - +
1119G SER* 2.8 16.4 + - - +
1121G LEU* 1.3 74.1 - - - +
1123G ARG* 1.3 71.9 + - - +
1125G SER* 3.8 8.7 + - - -
1126G SER* 2.8 43.2 + - - -
1127G ASP* 3.1 9.8 + - - +
1197G LEU* 5.2 12.1 - - - +
1200G LEU* 5.2 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100G LEU* 4.5 11.3 - - + +
1119G SER* 3.0 44.7 + - - +
1120G ILE* 4.0 10.1 - - + +
1121G LEU 3.1 1.0 - - - -
1122G ASN* 1.3 92.9 - - - +
1124G PHE* 1.3 59.6 + - + +
1127G ASP* 3.2 34.3 + - - +
1128G CYS* 2.9 26.5 + - - +
1313G ARG* 3.3 28.4 - - + +
1314G ILE* 3.6 21.8 - - + +
1317G LEU* 3.2 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495G ARG* 2.8 35.7 + - - +
499G THR* 4.6 19.7 - - + +
503G LEU* 5.4 4.7 - - + -
1097G HIS* 4.1 24.5 - + - -
1100G LEU* 3.5 34.8 - - + -
1101G LEU* 3.6 46.9 - - + -
1104G ILE* 3.8 25.6 - - + -
1120G ILE* 3.7 20.0 - - + -
1121G LEU* 3.1 8.7 + - - +
1123G ARG* 1.3 79.5 - - + +
1125G SER* 1.3 65.2 + - - +
1128G CYS* 3.7 13.7 - - + +
1129G ASN 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419G ASN* 5.2 7.4 + - - -
423G ILE* 6.1 0.3 - - - +
492G SER* 5.7 0.2 + - - -
495G ARG* 4.2 2.1 + - - -
496G LEU* 3.5 33.0 - - - +
500G ASN* 5.7 0.7 - - - -
1121G LEU* 2.9 26.5 + - - -
1122G ASN* 3.1 12.4 + - - -
1124G PHE* 1.3 81.9 - - - +
1126G SER* 1.3 59.4 + - - +
1129G ASN* 3.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G ILE* 4.3 20.1 - - - +
1122G ASN* 2.8 25.1 + - - -
1125G SER* 1.3 76.5 - - - +
1127G ASP* 1.3 64.3 + - - +
1128G CYS 3.5 0.9 - - - -
1129G ASN* 3.4 7.9 - - - +
1130G THR* 2.8 38.9 + - - -
----------------------------------------------------------
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