Contacts of the helix formed by residues 76 - 89 (chain A) in PDB entry 4L8E
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 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 3.9 18.9 + - - -
58A PRO 3.8 6.1 + - - -
75A PHE* 1.3 100.5 - - + +
77A SER* 1.3 66.8 + - - +
78A GLY* 4.5 1.8 + - - +
79A ALA* 3.1 13.9 + - + +
80A ILE* 3.0 24.1 + - - +
110A VAL* 5.6 3.3 - - - +
302A GSH 2.8 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 4.2 0.9 - - - -
19A LYS* 2.9 37.9 + - - +
20A ILE* 3.8 8.2 - - - +
58A PRO* 3.8 24.7 - - - +
76A GLU* 1.3 70.6 - - - +
78A GLY* 1.3 57.7 + - - +
80A ILE* 3.3 2.7 + - - +
81A LEU* 2.9 35.7 + - - +
110A VAL* 4.4 1.0 - - - +
302A GSH 2.5 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.2 3.2 + - - +
77A SER* 1.3 81.9 + - - +
79A ALA* 1.3 56.4 + - - +
81A LEU* 3.4 2.6 + - - +
82A LEU* 3.0 28.9 + - - +
106A LEU* 4.0 20.9 - - - +
110A VAL* 4.0 23.6 - - - +
302A GSH 4.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.9 12.2 - - + +
75A PHE 3.7 13.2 - - - +
76A GLU* 3.1 17.0 + - + +
78A GLY* 1.3 72.8 - - - +
80A ILE* 1.3 62.8 + - - +
82A LEU* 3.5 8.2 + - - +
83A TYR* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.7 16.2 - - + -
58A PRO* 3.7 33.0 - - + +
59A ALA* 3.8 8.5 - - - +
60A ILE* 4.0 22.7 - - + +
74A ILE* 3.7 38.8 - - + +
75A PHE 4.3 0.2 - - - -
76A GLU 3.0 17.1 + - - +
77A SER 3.6 4.9 - - - +
79A ALA* 1.3 74.6 - - - +
81A LEU* 1.3 60.7 + - - +
83A TYR* 3.3 4.4 + - - +
84A LEU* 2.9 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 3.8 22.4 - - + +
20A ILE* 3.9 11.7 - - + -
23A PHE* 3.8 35.8 - - + -
77A SER 2.9 22.5 + - - +
78A GLY 3.8 3.8 - - - +
80A ILE* 1.3 78.1 - - - +
82A LEU* 1.3 57.5 + - - +
84A LEU* 3.9 3.4 - - + +
85A ALA* 2.9 32.4 + - - +
106A LEU* 4.2 7.2 - - + -
166A ILE* 4.0 37.9 - - + +
169A ILE* 4.1 5.6 - - + -
170A ALA* 4.1 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY 3.0 17.7 + - - +
79A ALA* 3.8 7.9 - - - +
80A ILE 3.3 0.2 - - - -
81A LEU* 1.3 77.7 - - - +
83A TYR* 1.3 63.3 + - - +
85A ALA* 3.4 0.7 + - - +
86A ASN* 3.0 44.9 + - - +
92A LEU* 3.6 26.5 - - + -
99A ARG* 4.2 5.2 - - - +
103A LEU* 4.0 19.1 - - + -
106A LEU* 4.9 3.4 - - + -
107A PHE* 5.8 8.5 - - + -
166A ILE* 4.2 8.9 - - + +
304A CL 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 4.3 2.9 - - + -
62A ASP* 2.6 39.9 + - + +
65A PRO* 4.0 6.2 - - - +
66A ASP 5.0 0.9 + - - -
72A ILE* 3.7 32.2 - - + +
74A ILE* 3.3 32.3 - - + -
79A ALA 2.9 18.7 + - - +
80A ILE 3.7 2.0 - - - +
82A LEU* 1.3 78.3 - - - +
84A LEU* 1.3 74.3 + - + +
86A ASN* 3.4 7.3 + - + +
87A LYS* 2.9 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.3 11.7 - - + -
20A ILE* 4.3 10.1 - - + -
23A PHE* 3.5 31.4 - - + -
24A LEU* 4.1 14.8 - - + -
29A LEU* 4.3 20.6 - - + -
60A ILE* 4.2 13.2 - - + -
80A ILE* 2.9 39.9 + - + +
81A LEU* 4.0 2.9 - - - +
83A TYR* 1.3 89.3 - - + +
85A ALA* 1.3 65.5 + - - +
87A LYS* 3.8 6.9 - - + +
88A THR* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.8 3.1 - - + -
81A LEU 2.9 20.1 + - - +
82A LEU 3.8 2.9 - - - +
84A LEU* 1.3 75.9 - - - +
86A ASN* 1.3 58.5 + - - +
88A THR* 3.9 1.6 - - - -
89A GLY* 2.8 31.0 + - - -
90A ARG 3.4 23.8 + - - +
92A LEU* 3.8 24.8 - - + +
166A ILE* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.0 37.4 + - - +
83A TYR* 3.7 6.9 - - + +
85A ALA* 1.3 76.6 - - - +
87A LYS* 1.3 65.8 + - - +
88A THR 3.5 0.2 + - - -
89A GLY* 3.6 6.7 + - - -
92A LEU* 4.0 5.4 - - - +
94A LYS* 5.1 4.4 + - - +
99A ARG* 2.8 32.2 + - - +
304A CL 4.0 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.6 5.6 - - + +
29A LEU* 5.7 5.8 - - + +
62A ASP* 2.8 36.0 + - - +
64A GLN* 2.9 25.2 + - - +
66A ASP* 3.7 39.7 - - - +
83A TYR* 2.9 30.9 + - + +
84A LEU* 3.4 14.5 + - + +
86A ASN* 1.3 78.9 - - - +
88A THR* 1.3 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.7 9.4 - - + -
27A VAL* 4.2 20.6 - - + -
29A LEU* 4.2 26.2 - - + -
84A LEU* 2.8 22.3 + - - +
85A ALA 3.5 0.5 + - - -
87A LYS* 1.3 83.1 - - + +
89A GLY* 1.3 62.7 + - - +
90A ARG* 3.2 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA 2.8 14.0 + - - -
86A ASN* 3.6 3.4 + - - -
87A LYS 3.5 2.4 - - - -
88A THR* 1.3 77.0 - - - +
90A ARG* 1.3 62.6 + - - +
91A PHE 4.4 0.2 + - - -
92A LEU 4.6 7.0 - - - +
94A LYS* 3.9 35.2 - - - -
----------------------------------------------------------
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