Contacts of the helix formed by residues 74 - 88 (chain A) in PDB entry 4TMU
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 LEU 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 3.3 3.1 + - - -
73A PRO* 1.3 96.6 - - + +
75A ILE* 1.3 65.4 + - - +
76A SER* 4.2 10.8 - - - +
77A LEU* 3.2 22.7 + - + +
78A MET* 3.0 25.9 + - - +
154A TRP* 4.8 0.2 - - + -
298A MET* 3.7 54.7 - - + +
27B G 3.6 37.0 - - - +
28B C 3.5 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 1.3 69.8 - - - +
76A SER* 1.3 59.3 + - - +
78A MET* 3.3 16.0 + - + +
79A LYS* 3.0 30.7 + - + +
96A ASN* 3.3 49.1 - - + +
97A SER* 5.7 0.9 - - - +
98A THR* 4.8 13.5 - - + +
122A ALA* 5.5 1.8 - - + -
28B C 2.9 48.9 + - - +
29B C 4.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.2 15.5 - - - +
75A ILE* 1.3 82.2 - - - +
77A LEU* 1.3 61.0 + - - +
79A LYS* 3.9 7.2 - - - +
80A ASP* 3.1 36.1 + - - +
279A GLN* 5.7 2.8 + - - -
298A MET 5.1 2.3 + - - -
299A GLY 5.4 2.4 + - - -
28B C 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 4.8 5.6 - - - -
73A PRO* 3.8 30.5 - - + -
74A LEU* 3.2 24.5 + - + +
76A SER* 1.3 83.0 + - - +
78A MET* 1.3 67.4 + - - +
80A ASP* 3.2 7.8 + - + +
81A GLN* 3.0 42.9 + - + +
146A ASP* 6.4 0.2 - - + -
147A GLU* 4.0 23.6 - - + +
298A MET* 4.0 7.0 - - + +
299A GLY* 3.2 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 3.7 16.7 - - - +
74A LEU 3.0 13.9 + - - +
75A ILE* 3.3 22.2 + - + +
77A LEU* 1.3 74.8 - - - +
79A LYS* 1.3 57.8 - - - +
81A GLN* 3.4 1.2 + - - +
82A VAL* 2.9 35.9 + - - +
94A CYS* 3.5 17.5 - - + -
95A LEU 3.2 22.0 - - - +
96A ASN* 2.9 34.3 - - + +
120A TYR* 3.5 28.5 - - + -
121A ILE* 4.1 19.5 - - - -
122A ALA* 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 3.0 20.0 + - + +
76A SER* 3.9 8.1 - - - +
78A MET* 1.3 74.9 - - - +
80A ASP* 1.3 69.5 + - - +
82A VAL* 4.7 3.4 - - - -
83A ASP* 2.9 51.3 + - - +
94A CYS* 5.2 4.7 - - - -
----------------------------------------------------------
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 SER* 3.1 26.1 + - - +
77A LEU* 3.2 12.2 + - + +
79A LYS* 1.3 80.8 - - - +
81A GLN* 1.3 64.2 + - + +
83A ASP* 3.9 4.7 - - - +
84A GLN* 3.2 29.3 + - - +
279A GLN* 5.8 0.5 + - - -
299A GLY* 4.6 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 3.0 17.2 + - - -
57A TYR* 2.8 27.1 + - - -
58A GLN* 3.9 6.3 + - - +
72A SER* 5.5 2.6 + - - -
77A LEU* 3.0 30.1 + - + +
78A MET 4.1 0.4 - - - +
80A ASP* 1.3 78.3 - - + +
82A VAL* 1.3 65.6 + - - +
84A GLN* 3.5 12.9 + - - +
85A LEU* 3.1 29.7 + - - +
120A TYR* 3.4 26.4 + - + +
146A ASP* 3.3 15.6 + - - +
147A GLU* 5.6 1.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
78A MET 2.9 20.9 + - - +
79A LYS* 4.1 3.6 - - - +
81A GLN* 1.3 74.7 - - - +
83A ASP* 1.3 62.6 + - - +
85A LEU* 3.2 3.2 + - - +
86A LEU* 2.9 51.7 + - + +
92A ALA* 4.0 19.5 - - + +
93A ALA* 3.6 33.4 - - - +
94A CYS* 4.1 12.6 - - + +
120A TYR* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS* 2.9 52.7 + - - +
80A ASP* 3.9 4.7 - - - +
82A VAL* 1.3 84.2 - - - +
84A GLN* 1.3 56.4 + - - +
86A LEU* 3.2 15.1 + - - +
87A ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 3.2 20.4 + - - +
81A GLN* 3.8 13.0 - - - +
83A ASP* 1.3 77.8 - - - +
85A LEU* 1.3 64.6 + - + +
87A ALA* 3.3 9.0 + - - +
88A ASN* 3.2 28.9 + - - +
301A ASN* 5.9 3.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
21A PHE* 4.4 13.7 - - + -
58A GLN* 3.6 42.4 - - + +
62A LEU* 5.5 0.4 - - + -
81A GLN 3.1 20.7 + - - +
82A VAL 3.2 4.2 + - - +
84A GLN* 1.3 77.2 - - + +
86A LEU* 1.3 61.9 + - - +
88A ASN* 3.1 12.3 + - - +
90A VAL* 3.0 48.9 + - + +
92A ALA* 3.7 26.0 - - + -
118A LEU* 4.4 10.8 - - + -
120A TYR* 3.7 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 2.9 37.8 + - + +
83A ASP* 3.5 14.8 - - - +
85A LEU* 1.3 75.5 - - - +
87A ALA* 1.3 57.9 + - - +
89A GLY* 2.9 19.3 + - - -
90A VAL 3.6 18.4 - - - +
91A ALA* 5.1 1.3 - - - -
92A ALA* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP 2.9 12.8 + - - +
84A GLN* 3.5 13.0 - - - +
85A LEU 3.3 0.2 - - - -
86A LEU* 1.3 76.5 - - - +
88A ASN* 1.3 60.2 + - - +
89A GLY 3.5 1.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
20A THR* 3.5 36.5 - - - +
21A PHE* 4.0 25.6 - - - -
84A GLN* 3.2 21.1 + - - +
85A LEU* 3.1 11.0 + - - +
87A ALA* 1.3 77.8 - - - +
89A GLY* 1.3 60.9 + - - +
90A VAL* 3.3 13.5 + - + +
----------------------------------------------------------
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