Contacts of the helix formed by residues 117 - 123 (chain C) in PDB entry 4LQL
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 ASP 117 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LYS* 4.1 25.6 - - + +
419B LEU* 4.5 5.6 - - - +
115C SER 3.3 7.8 + - - +
116C ILE* 1.3 77.7 - - - +
118C MET* 1.3 56.2 + - - +
119C ASP* 3.4 21.2 - - - +
120C TYR* 2.9 22.9 + - - +
121C MET* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TYR* 3.5 17.9 - - - +
349B MET* 3.4 28.3 - - - +
366B HIS 5.2 7.9 - - - +
367B PRO 5.5 6.3 - - - +
368B LEU* 4.5 16.2 - - + -
370B ILE* 6.4 2.2 - - + -
378B ARG* 4.9 3.6 - - - +
419B LEU* 5.4 1.6 - - - -
420B PRO* 4.3 21.4 - - + +
421B VAL* 3.4 25.1 - - + -
117C ASP* 1.3 73.4 - - - +
119C ASP* 1.3 57.0 + - - +
121C MET* 3.1 12.9 - - - +
122C ASN* 2.4 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASP* 3.2 20.3 - - - +
118C MET* 1.3 76.5 - - - +
120C TYR* 1.3 62.1 + - - +
122C ASN* 3.3 21.0 - - - +
123C LEU* 3.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PRO* 5.4 4.9 - - + -
115C SER 5.1 0.2 - - - +
116C ILE* 3.3 36.6 - - + -
117C ASP* 2.9 26.2 + - - +
118C MET 3.1 0.2 - - - -
119C ASP* 1.3 76.8 - - - +
121C MET* 1.3 49.2 + - - +
122C ASN 3.1 0.2 - - - -
123C LEU* 2.6 39.5 + - - +
124C HIS* 4.4 14.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TYR* 3.3 60.8 - - + +
334B THR* 5.1 9.9 - - + -
419B LEU* 3.4 32.3 - - + -
116C ILE* 3.5 29.4 - - + -
117C ASP 2.8 14.8 + - - +
118C MET* 3.0 16.8 + - - +
120C TYR* 1.3 72.2 - - - +
122C ASN* 1.3 64.9 + - - +
123C LEU 3.1 10.2 - - - +
124C HIS 5.6 3.4 - - - +
125C GLN* 3.1 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 5.7 2.8 - - - -
23C ALA* 5.3 12.1 - - + +
82C THR* 3.9 5.4 - - - +
118C MET 2.4 22.1 + - - +
119C ASP* 3.3 20.0 - - - +
120C TYR 3.1 0.2 - - - -
121C MET* 1.3 70.3 - - - +
123C LEU* 1.3 61.8 + - + +
125C GLN* 3.3 22.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 6.1 0.9 - - + -
23C ALA* 3.3 27.6 - - + +
24C LEU* 5.0 3.6 - - + -
26C GLU* 3.6 28.3 - - + -
27C VAL* 3.4 23.1 - - + +
30C ASP* 4.8 3.6 - - - -
81C HIS* 3.3 31.4 - - + +
82C THR* 3.6 14.1 - - + -
119C ASP 3.9 2.4 + - - +
120C TYR* 2.6 24.8 + - - +
121C MET* 3.2 13.2 - - - +
122C ASN* 1.3 81.1 - - + +
124C HIS* 1.3 68.0 + - + +
125C GLN* 2.9 7.6 + - - +
----------------------------------------------------------
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