Contacts of the helix formed by residues 95 - 105 (chain A) in PDB entry 5C5A
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 GLU 95 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.6 8.4 - - + -
92A SER* 2.8 45.2 + - - +
93A VAL 3.2 0.4 - - - -
94A LYS* 1.3 77.6 - - + +
96A HIS* 1.3 63.5 + - - +
97A ARG 3.4 2.5 - - - -
98A LYS* 2.7 45.2 + - + -
99A ILE* 3.0 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL 3.0 28.5 + - - -
94A LYS* 2.9 16.8 + - - +
95A GLU* 1.3 72.8 - - - +
97A ARG* 1.3 62.6 + - - +
99A ILE 3.8 0.2 - - - -
100A TYR* 2.9 37.3 + - + -
201A NUT 3.4 44.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU 3.4 0.4 - - - -
96A HIS* 1.3 76.8 - - - +
98A LYS* 1.3 59.2 + - - +
100A TYR* 3.5 3.7 + - - +
101A THR* 2.9 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 5.2 16.6 - - + +
90A SER 5.0 4.0 + - - +
91A PHE* 4.2 18.8 - - + +
95A GLU* 2.7 47.8 + - + +
96A HIS 3.3 0.4 - - - -
97A ARG* 1.3 80.6 - - - +
99A ILE* 1.3 58.3 + - + +
101A THR* 3.2 6.5 + - - -
102A MET* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.1 3.8 - - + -
86A PHE* 4.5 6.7 - - + -
91A PHE* 3.8 30.1 - - + -
92A SER 3.7 19.5 - - - +
93A VAL* 3.9 8.3 - - - +
95A GLU* 3.0 17.5 + - + +
96A HIS 3.9 3.1 - - - +
98A LYS* 1.3 79.0 - - + +
100A TYR* 1.3 64.9 + - - +
102A MET* 3.9 3.9 - - - +
103A ILE* 2.9 46.1 + - + +
201A NUT 3.6 52.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.1 25.7 - - + +
54A LEU* 3.5 21.2 - - + +
96A HIS* 2.9 34.1 + - + +
97A ARG* 4.0 4.7 - - - +
99A ILE* 1.3 76.9 - - - +
101A THR* 1.3 59.5 + - + +
103A ILE* 3.2 6.6 + - - +
104A TYR* 2.9 57.4 + + + -
201A NUT 3.3 26.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 2.9 50.3 + - + +
98A LYS* 3.2 10.6 + - - -
100A TYR* 1.3 73.3 - - + +
102A MET* 1.3 78.0 + - - +
104A TYR* 3.3 10.4 + - + +
105A ARG* 3.1 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.3 54.1 - - + +
88A VAL* 5.1 9.4 - - + -
98A LYS* 2.9 34.1 + - + +
99A ILE 4.0 3.1 - - - +
101A THR* 1.3 96.3 + - - +
103A ILE* 1.3 66.3 + - - +
105A ARG* 3.1 51.9 + - - +
106A ASN* 2.9 24.6 + - - +
202A SO4 5.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.9 3.1 - - + +
50A MET* 3.8 18.6 - - - -
53A VAL* 4.1 11.4 - - + -
54A LEU* 3.5 33.7 - - + -
57A LEU* 3.6 28.5 - - + -
86A PHE* 3.8 12.1 - - + -
99A ILE* 2.9 31.5 + - + +
100A TYR* 3.6 5.8 - - - +
102A MET* 1.3 76.1 - - - +
104A TYR* 1.3 58.3 + - - +
106A ASN* 2.9 23.6 + - - +
107A LEU* 3.4 28.4 - - + +
201A NUT 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 4.5 12.5 + - + +
50A MET* 3.6 26.9 - - + +
100A TYR* 2.9 50.4 + + + +
101A THR* 3.8 9.4 - - + +
102A MET 3.3 0.2 - - - -
103A ILE* 1.3 75.7 - - - +
105A ARG* 1.3 57.0 + - - +
106A ASN 3.0 0.6 + - - -
107A LEU* 3.0 42.4 - - + +
109A VAL* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.1 23.1 + - - +
101A THR* 3.1 21.4 + - - +
102A MET* 3.5 43.0 - - - +
103A ILE 3.1 0.8 - - - -
104A TYR* 1.3 75.8 - - + +
106A ASN* 1.3 63.2 + - - +
107A LEU 3.6 1.1 - - - -
202A SO4 2.9 43.0 + - - -
----------------------------------------------------------
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