Contacts of the helix formed by residues 93 - 101 (chain A) in PDB entry 2CFZ
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 PRO 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 3.3 43.1 - - + +
35A ARG* 5.3 1.6 - - - +
37A VAL* 4.0 9.0 - - + -
38A GLU* 4.0 21.5 - - + +
43A PHE* 3.5 26.0 - - + -
87A PRO* 5.5 6.7 - - + -
91A ILE 3.1 7.8 - - - +
92A ASN* 1.4 90.0 - - - +
94A SER* 1.3 55.1 + - - +
96A GLN* 3.7 10.3 - - + +
97A ARG* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 4.0 3.3 - - - +
41A LEU* 3.8 16.6 - - - -
43A PHE* 3.7 9.7 - - - -
92A ASN* 2.8 12.4 + - - -
93A PRO* 1.3 77.8 - - - +
95A LEU* 1.3 65.7 + - - +
97A ARG* 3.2 4.2 + - - +
98A GLN 3.1 13.7 + - - -
399A TRP* 3.5 8.1 - - - -
404A TYR* 2.8 34.8 + - - -
501A GLU* 2.5 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.5 4.9 - - + -
92A ASN* 3.0 16.5 + - + +
94A SER* 1.3 80.1 + - - +
96A GLN* 1.3 56.3 + - - +
98A GLN* 3.2 3.4 + - + +
99A ALA* 2.8 27.3 + - - +
235A VAL* 3.9 15.5 - - + -
236A ASP* 4.3 16.4 - - + +
404A TYR* 3.8 17.3 - - + -
500A ALA 3.7 15.3 - - - +
501A GLU* 3.5 22.0 - - - +
503A ALA* 4.0 28.3 - - + -
506A ARG* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE 5.7 0.2 + - - -
82A LEU* 3.9 28.5 + - + +
85A GLY* 4.4 9.4 + - - -
86A LYS 2.7 28.9 + - - -
87A PRO* 3.4 7.0 - - - +
88A ARG* 2.9 37.8 + - - +
91A ILE* 3.7 21.6 - - + +
92A ASN 2.8 18.5 + - - +
93A PRO* 3.8 9.1 - - + +
94A SER 3.2 0.4 - - - -
95A LEU* 1.3 74.0 - - - +
97A ARG* 1.3 60.6 + - - +
99A ALA* 3.5 4.9 - - - +
100A LEU* 3.2 23.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
43A PHE* 4.3 15.1 + - + -
45A ASP* 3.0 26.1 + - - -
46A ARG* 4.1 5.5 - - - +
48A ASP* 3.1 40.6 + - - +
49A PHE* 3.9 26.2 - - + -
93A PRO 3.1 13.6 + - - +
94A SER 3.2 8.9 + - - +
96A GLN* 1.3 75.5 - - - +
98A GLN* 1.3 67.2 + - - +
100A LEU* 3.3 6.1 + - - +
101A LEU* 3.0 42.1 + - + +
399A TRP* 3.2 57.6 - - - +
404A TYR* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER 3.1 2.8 + - - -
95A LEU* 3.5 8.3 - - + +
97A ARG* 1.3 82.0 - - - +
99A ALA* 1.3 57.8 + - - +
101A LEU* 3.2 8.8 + - - +
102A ASN* 2.9 31.5 + - - +
236A ASP* 3.8 15.0 - - - +
238A ALA* 3.1 21.7 - - - +
303A GLY 3.0 21.1 + - - +
345A ASN* 3.6 7.1 - - - +
346A TRP* 3.6 24.9 - - - -
399A TRP* 5.3 1.8 + - - +
404A TYR* 3.4 49.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.9 16.3 - - + +
95A LEU 2.8 20.3 + - - +
96A GLN* 3.5 11.2 - - - +
97A ARG 3.3 0.2 - - - -
98A GLN* 1.3 74.2 - - - +
100A LEU* 1.3 60.7 + - - +
102A ASN* 3.6 0.9 + - - +
103A LEU* 3.5 14.6 + - - +
235A VAL* 3.7 24.7 - - + +
236A ASP* 3.6 17.9 + - + -
241A LYS* 2.9 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 4.1 24.2 - - + -
82A LEU* 3.7 30.9 - - + +
83A LEU* 4.3 19.3 - - + +
85A GLY* 4.0 19.7 - - - +
96A GLN* 3.2 11.0 + - + +
97A ARG* 3.7 8.1 - - - +
99A ALA* 1.3 78.0 - - - +
101A LEU* 1.3 60.7 + - - +
103A LEU* 2.9 39.2 + - + +
104A LYS* 3.6 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 3.5 35.7 - - + +
49A PHE* 3.7 26.0 - - + +
52A ALA* 3.8 12.7 - - + +
97A ARG* 3.0 53.9 + - + +
98A GLN* 3.2 11.0 + - - +
100A LEU* 1.3 74.5 - - - +
102A ASN* 1.3 58.6 + - - +
104A LYS* 3.0 31.1 + - + +
118A ARG* 5.3 0.9 + - - -
346A TRP* 3.6 34.8 - - + -
----------------------------------------------------------
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