Contacts of the helix formed by residues 92 - 100 (chain C) in PDB entry 4LXZ
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 TYR 92 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PHE* 3.9 20.9 - + + -
83C SER* 3.5 31.4 + - - -
84C ILE* 3.6 21.5 - - + -
88C ASN* 3.5 44.5 + - - -
89C MET 3.0 7.7 + - - +
91C GLU* 1.4 92.3 + - + +
93C SER* 1.4 51.9 + - - +
94C LYS 3.4 2.2 - - - -
95C GLN* 3.2 31.1 + - + -
96C MET* 2.7 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C MET 3.3 7.7 + - - -
90C SER* 3.9 12.8 + - - -
91C GLU 3.7 3.1 - - - -
92C TYR* 1.4 76.0 - - - +
94C LYS* 1.3 77.4 + - - +
96C MET* 3.4 9.7 + - - +
97C GLN* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 6.2 1.3 - - + -
377A MET* 3.5 35.2 + - + +
92C TYR 3.4 0.6 - - - -
93C SER* 1.3 91.4 + - - +
95C GLN* 1.4 65.9 + - - +
97C GLN* 3.3 28.5 + - - +
98C ARG* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PHE* 3.6 23.3 - - + -
91C GLU 3.9 9.5 + - - +
92C TYR* 3.4 45.3 - - + +
94C LYS* 1.4 80.3 + - - +
96C MET* 1.3 60.2 + - - +
98C ARG* 3.3 15.4 + - - +
99C PHE* 2.9 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PHE* 3.7 23.1 - - + -
84C ILE* 4.5 3.8 - - + -
89C MET* 3.7 55.0 - - + +
92C TYR 2.7 19.5 + - - +
93C SER* 3.6 9.4 - - - +
94C LYS 3.3 0.2 - - - -
95C GLN* 1.3 73.3 - - - +
97C GLN* 1.3 56.3 + - - +
100C ASN* 2.9 24.6 + - - -
101C VAL* 2.9 38.1 + - + +
102C GLY* 3.8 15.5 - - - -
107C VAL* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 2.9 36.5 + - - +
377A MET* 3.4 17.0 + - - -
378A LEU 3.0 21.8 + - - -
379A PRO* 4.8 2.6 - - - +
93C SER 3.1 12.4 + - - +
94C LYS* 3.5 31.4 + - - +
95C GLN 3.3 0.2 - - - -
96C MET* 1.3 75.6 - - - +
98C ARG* 1.3 64.4 + - - +
99C PHE 3.4 0.3 + - - -
100C ASN* 3.5 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LYS* 5.6 0.2 - - - +
226A TYR* 2.9 29.9 + - - -
373A GLU* 4.2 24.4 + - - +
374A ASN* 5.8 1.8 + - - -
376A ARG* 2.9 37.3 + - - +
377A MET* 3.6 29.0 - - - +
76C GLU* 6.2 0.4 - - - -
94C LYS* 3.0 34.1 + - - +
95C GLN* 3.3 16.9 + - - +
97C GLN* 1.3 77.7 - - - +
99C PHE* 1.3 84.5 + - + +
150C SER 3.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 4.5 2.5 - - - -
74C SER* 4.7 0.4 - - - -
76C GLU* 3.8 29.2 - - + -
77C TYR* 3.5 33.7 - + + -
80C PHE* 3.5 44.2 - + + -
95C GLN* 2.9 38.7 + - + +
98C ARG* 1.3 103.0 - - + +
100C ASN* 1.4 62.4 + - - +
101C VAL* 3.4 2.0 + - - +
150C SER* 3.3 27.8 - - - -
151C GLU* 4.1 1.8 - - - -
152C ALA* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 5.4 1.1 - - - -
96C MET 2.9 7.8 + - - -
97C GLN* 3.5 9.2 + - - +
98C ARG 3.5 0.4 - - - +
99C PHE* 1.4 79.9 - - - +
101C VAL* 1.3 59.3 + - - +
103C GLU* 5.1 13.7 + - - +
104C ASP* 5.8 4.3 + - - +
105C CYS* 4.0 10.5 + - - +
151C GLU* 3.5 22.4 + - - +
152C ALA* 2.9 33.5 + - - +
153C SER* 4.1 9.5 + - - +
----------------------------------------------------------
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