Contacts of the helix formed by residues 75 - 90 (chain A) in PDB entry 5MQI
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 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.4 26.1 + - - +
32A LEU* 5.5 3.0 - - - +
72A HIS* 3.4 12.6 + - + +
73A HIS 3.4 1.5 - - - -
74A GLN* 1.3 72.1 - - - +
76A LYS* 1.3 64.3 + - - +
77A PRO* 3.1 25.1 - - - +
78A LEU* 3.2 22.9 - - + +
79A PHE* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS 4.8 3.8 - - - +
74A GLN* 3.1 15.8 + - - +
75A ASP* 1.3 71.4 - - - +
77A PRO* 1.3 73.0 - - + +
79A PHE* 3.5 5.9 + - - +
80A ASP* 3.1 24.3 + - - +
151A GLU* 5.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.5 26.4 - - + +
36A LYS* 5.6 2.1 - - - +
75A ASP* 3.1 16.6 - - - +
76A LYS* 1.3 94.2 - - + +
78A LEU* 1.3 55.0 + - - +
80A ASP* 3.5 6.4 + - + +
81A ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.6 29.6 - - + +
31A CYS* 3.9 16.8 - - + -
32A LEU* 3.7 39.4 - - + +
35A VAL* 4.0 6.5 - - + -
68A ILE* 3.6 19.7 - - + -
72A HIS* 4.6 4.0 - - + +
75A ASP* 3.2 32.5 + - + +
76A LYS 3.3 0.4 - - - -
77A PRO* 1.3 78.9 - - - +
79A PHE* 1.3 60.4 + - - +
81A ALA* 3.1 2.6 + - - +
82A VAL* 2.9 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 5.5 2.5 - - - -
69A LEU* 3.3 29.4 - - + +
72A HIS 4.7 2.2 + - - +
73A HIS* 3.5 32.5 - - + +
75A ASP 3.0 17.0 + - - +
76A LYS* 3.8 6.3 - - - +
78A LEU* 1.3 76.2 - - - +
80A ASP* 1.3 61.5 + - + +
82A VAL* 3.3 7.7 + - - +
83A ILE* 3.0 56.9 + - + +
132A VAL* 3.5 22.2 - - + -
133A LEU* 4.7 5.6 - - + -
136A THR* 3.6 36.8 - - + -
155A LEU* 4.3 13.7 - - + -
159A ILE* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS 3.1 17.4 + - - +
77A PRO* 3.7 6.7 - - + +
79A PHE* 1.3 82.0 - - + +
81A ALA* 1.3 62.5 + - - +
83A ILE* 3.5 6.4 + - - +
84A ARG* 3.2 24.8 + - - +
151A GLU* 4.4 20.9 - - - +
154A LEU* 6.2 0.2 - - - +
155A LEU* 4.0 31.6 - - + +
158A ARG* 3.7 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.6 20.2 - - + -
35A VAL* 3.7 18.3 - - + +
36A LYS* 4.4 12.8 - - + -
39A ILE* 3.7 9.5 - - + +
77A PRO 3.0 15.2 + - - +
78A LEU 3.1 7.6 + - - +
80A ASP* 1.3 75.8 + - - +
82A VAL* 1.3 63.4 + - - +
84A ARG* 3.3 11.9 + - - +
85A LEU* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.1 17.7 - - + -
65A LEU* 3.7 40.6 - - + +
68A ILE* 3.7 26.2 - - + -
69A LEU* 4.6 9.0 - - + +
78A LEU* 2.9 29.8 + - + +
79A PHE* 3.3 6.7 + - - +
81A ALA* 1.3 72.7 - - - +
83A ILE* 1.3 64.8 + - - +
85A LEU* 3.3 4.0 + - - +
86A MET* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.5 26.7 - - + -
79A PHE* 3.0 40.6 + - + +
80A ASP 3.7 5.8 - - - +
81A ALA 3.3 0.2 - - - -
82A VAL* 1.3 75.5 - - - +
84A ARG* 1.3 57.3 + - - +
86A MET* 3.0 13.6 + - + +
87A VAL* 2.8 29.8 + - + +
133A LEU* 3.8 23.1 - - + -
155A LEU* 4.3 11.4 - - + -
158A ARG* 3.7 38.6 - - + +
159A ILE* 4.4 5.4 - - + +
162A LEU* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 5.6 1.4 - - - +
39A ILE* 3.5 39.1 - - + +
43A ARG* 4.6 10.7 - - - +
80A ASP* 3.2 15.0 + - - +
81A ALA* 3.3 11.6 + - - +
83A ILE* 1.3 79.1 - - - +
85A LEU* 1.3 61.2 + - - +
87A VAL* 3.5 6.2 + - - +
88A ASN* 3.2 21.8 + - - +
158A ARG* 3.3 53.8 - - - +
1603A SO4 2.5 45.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.1 11.7 - - + +
38A LEU* 4.0 33.4 - - + -
39A ILE* 3.9 21.4 - - + +
42A LEU* 3.4 32.5 - - + -
55A LEU* 5.1 1.3 - - + -
60A ILE* 5.5 0.2 - - + -
65A LEU* 3.4 39.0 - - + -
81A ALA 3.1 10.3 + - - +
82A VAL* 3.3 8.9 + - - +
84A ARG* 1.3 77.7 - - - +
86A MET* 1.3 57.8 + - - +
88A ASN* 3.3 3.8 + - - +
89A LEU* 2.9 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.0 20.4 - - + -
65A LEU* 4.2 25.6 - - + -
66A LEU* 4.8 3.1 - - - -
69A LEU* 3.8 35.4 - - + -
82A VAL* 2.9 28.1 + - + +
83A ILE* 3.6 9.0 - - + +
85A LEU* 1.3 73.2 - - - +
87A VAL* 1.3 63.0 + - - +
89A LEU* 3.3 6.0 + - - -
90A THR* 2.8 33.2 + - - +
124A PHE* 3.9 16.8 - - + -
162A LEU* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 2.8 20.9 + - + +
84A ARG* 3.7 7.0 - - - +
85A LEU 3.3 0.4 - - - -
86A MET* 1.3 75.0 - - - +
88A ASN* 1.3 65.0 + - - +
90A THR* 3.2 9.2 + - - -
91A GLN* 3.4 8.7 + - + +
158A ARG* 3.4 41.1 - - + +
161A LEU* 4.2 23.6 - - + -
162A LEU* 3.9 14.8 - - + +
165A ASN* 3.2 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 5.2 8.0 + - + +
42A LEU* 3.7 29.5 + - + +
43A ARG* 4.9 12.1 - - - +
52A ARG* 2.8 43.2 + - - +
84A ARG 3.2 11.9 + - - +
85A LEU* 3.6 8.3 - - - +
87A VAL* 1.3 81.3 - - - +
89A LEU* 1.3 60.0 + - - +
91A GLN* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.6 30.7 - - + -
52A ARG* 3.9 21.2 + - + +
55A LEU* 4.1 20.4 - - + -
60A ILE* 5.8 1.6 - - + -
61A LEU* 4.4 19.1 - - + +
65A LEU* 3.8 29.4 - - + -
85A LEU* 2.9 27.4 + - + +
86A MET* 3.9 5.2 - - - +
88A ASN* 1.3 75.2 - - - +
90A THR* 1.3 57.5 + - - +
91A GLN 3.3 1.3 + - - -
117A LEU* 3.5 9.5 - - - +
120A TYR* 3.5 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.3 16.8 - - + -
86A MET 2.8 22.8 + - - +
87A VAL* 3.2 3.3 + - - -
88A ASN 3.3 0.2 - - - -
89A LEU* 1.3 76.2 - - - +
91A GLN* 1.3 67.7 + - - +
92A PRO* 3.4 1.9 - - - +
117A LEU* 3.7 12.0 - - + +
120A TYR* 4.3 7.4 - - + -
124A PHE* 4.7 0.4 - - + -
162A LEU* 3.6 11.6 - - + +
165A ASN* 3.1 44.9 + - - +
166A ILE* 3.5 28.7 - - + -
169A VAL* 5.1 1.5 - - - +
----------------------------------------------------------
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