Contacts of the helix formed by residues 78 - 92 (chain A) in PDB entry 3LUE
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 ASN 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.4 15.7 - - - +
69A TYR* 2.7 43.7 + - - +
70A PRO* 3.6 14.1 + - + +
76A VAL* 3.5 10.4 - - - +
77A THR* 1.3 83.8 + - - +
79A TRP* 1.3 59.8 + - - +
80A ASP* 3.9 4.2 + - - +
81A ASP* 2.9 8.1 + - - +
82A MET* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.7 43.7 + - + -
77A THR 4.1 5.1 + - - -
78A ASN* 1.3 73.6 - - - +
80A ASP* 1.3 65.9 + - - +
82A MET* 3.6 5.0 + - + +
83A GLU* 3.0 29.5 + - - +
86A TRP* 4.1 20.6 - + - -
115A ASN* 4.1 34.3 - - + +
118A LYS* 3.4 48.4 - - + +
119A MET* 4.2 13.7 - - + -
122A ILE* 3.5 28.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
67A LEU 4.4 11.4 - - - +
68A LYS* 5.2 0.9 - - - -
69A TYR* 1.3 67.0 - - + +
78A ASN* 3.6 4.2 + - - -
79A TRP* 1.3 78.5 + - - +
81A ASP* 1.3 47.7 - - - +
83A GLU* 4.0 12.4 - - + +
84A LYS* 5.0 0.2 - - - -
118A LYS* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 1.7 50.9 - - + +
62A ARG* 4.8 0.4 + - - -
67A LEU* 3.2 30.5 - - - +
69A TYR* 0.4 442.1 + - + +
78A ASN* 2.9 10.2 + - - +
80A ASP* 1.3 65.7 - - - +
82A MET* 1.3 52.4 + - - +
84A LYS* 3.4 0.3 - - - +
85A ILE* 3.1 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN* 3.2 26.7 - - - +
17A CYS* 4.7 0.4 - - - -
69A TYR* 2.3 2.2 - - - -
70A PRO* 3.8 8.1 - - + +
71A ILE* 3.4 37.9 - - + -
76A VAL* 3.5 24.9 - - + -
78A ASN 3.1 19.5 + - - +
79A TRP* 3.9 8.1 - - + +
81A ASP* 1.3 73.3 - - - +
83A GLU* 1.3 62.8 + - - +
85A ILE* 2.8 43.5 + - + +
86A TRP* 3.1 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 2.9 21.2 - - + +
79A TRP 3.0 20.2 + - - +
80A ASP* 3.3 10.7 - - - +
82A MET* 1.3 73.7 - - - +
84A LYS* 1.3 65.5 + - - +
86A TRP* 3.3 10.6 + - - +
87A HIS* 3.1 20.8 + - - +
118A LYS* 4.5 6.1 + - - -
122A ILE* 3.9 36.6 - - + +
126A THR* 3.9 23.3 + - - +
127A PHE* 4.0 7.2 - - + -
120K LYS* 5.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 2.7 26.1 - - + +
35A VAL* 2.6 20.2 + - - +
67A LEU 2.9 5.3 - - - -
68A LYS* 0.4 253.1 + - + +
69A TYR* 0.8 210.1 - - + +
83A GLU* 1.3 64.2 - - - +
85A ILE* 1.3 63.0 + - - +
86A TRP 3.2 0.3 + - - -
87A HIS 3.3 0.7 + - - -
88A HIS* 3.0 20.4 + - - +
120K LYS* 4.6 0.2 - - + -
122K VAL* 3.4 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 3.9 16.4 - - - -
31A PHE* 4.0 12.8 - - + -
32A PRO 5.1 2.0 - - - +
33A SER* 4.2 30.5 - - - +
34A ILE* 5.1 11.9 - - + +
69A TYR* 4.8 0.9 - - + -
70A PRO* 3.6 25.8 - - + -
71A ILE* 5.0 0.7 - - + -
81A ASP 3.1 10.0 + - - +
82A MET* 2.8 35.6 + - + +
84A LYS* 1.3 75.3 - - - +
86A TRP* 1.3 61.0 + - + +
88A HIS* 3.2 9.6 + - - +
89A THR* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 20.5 - - + +
12A ASN* 2.9 38.3 + - - -
76A VAL* 5.6 1.6 - - + -
79A TRP* 4.1 17.7 - + - -
82A MET* 3.1 47.0 + - + +
83A GLU* 3.8 6.1 - - - +
85A ILE* 1.3 77.2 - - + +
87A HIS* 1.3 64.2 + - - +
89A THR* 2.8 29.3 + - - -
90A PHE* 3.1 15.3 + + + -
105A LEU* 4.4 10.3 - - + -
119A MET* 4.2 27.6 - - + -
122A ILE* 4.0 21.8 - - + -
123A MET* 3.5 27.6 - - + -
127A PHE* 3.9 12.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR 4.6 2.9 + - - +
83A GLU 3.1 12.7 + - - +
84A LYS* 3.4 10.5 - - - +
86A TRP* 1.3 72.6 - - - +
88A HIS* 1.3 58.0 + - - +
90A PHE* 3.5 0.8 + - - -
91A TYR* 2.9 76.1 + + + +
92A ASN* 5.4 2.7 - - - -
127A PHE* 3.7 18.3 - - + -
118K GLY 5.6 0.9 - - - -
119K VAL* 4.5 8.7 - - + -
120K LYS* 4.0 43.7 + - + +
122K VAL* 4.3 7.6 - - + -
143K THR* 4.2 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.2 21.8 - + - +
84A LYS 3.0 12.4 + - - +
85A ILE* 3.3 9.9 - - - +
87A HIS* 1.3 72.7 - - - +
89A THR* 1.3 57.7 + - - +
92A ASN* 3.0 46.4 + - + +
93A GLU* 2.7 64.9 + - - +
122K VAL* 4.3 18.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.9 21.9 - - + +
17A CYS* 5.7 0.2 - - - -
19A ALA* 3.7 30.5 - - + -
31A PHE* 3.5 17.3 - - + -
85A ILE* 2.8 17.5 + - - +
86A TRP* 2.8 27.2 + - - -
88A HIS* 1.3 73.2 - - - +
90A PHE* 1.3 58.4 + - + +
93A GLU* 3.3 8.2 + - - +
94A LEU* 2.7 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.3 34.3 - - + -
10A VAL* 4.5 17.0 - - + -
86A TRP* 3.1 30.9 + + + -
87A HIS* 4.1 1.3 - - - +
89A THR* 1.3 79.6 - - + +
91A TYR* 1.3 62.0 + + + +
94A LEU* 4.8 0.4 - - - -
95A ARG 2.8 30.3 + - - -
96A VAL* 2.8 24.4 + - + +
98A PRO* 3.6 33.0 - - + -
103A VAL* 4.0 17.3 - - + -
105A LEU* 5.6 0.2 - - + -
123A MET* 4.0 30.3 - - + -
127A PHE* 4.2 18.8 - + + -
142K TRP* 3.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 2.9 70.6 + + + +
90A PHE* 1.3 65.9 - - + +
92A ASN* 1.3 64.7 + - - +
95A ARG* 4.6 0.2 - - - -
96A VAL 4.0 0.9 - - - -
98A PRO* 3.7 25.3 - - + +
99A GLU* 4.8 3.8 + - - -
127A PHE* 4.1 20.1 + + - -
142K TRP* 1.2 86.2 - - + +
143K THR* 4.6 6.1 - - + +
146K LEU* 1.0 128.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 5.4 3.1 - - - -
88A HIS* 3.0 44.2 + - + +
91A TYR* 1.3 95.6 + - - +
93A GLU* 1.3 73.0 + - - +
95A ARG* 3.5 17.8 - - - +
43K TRP* 4.6 4.7 - - - -
47K GLN* 4.3 4.9 + - - +
122K VAL* 5.0 5.9 - - - +
124K ILE* 4.2 13.7 - - - +
139K GLY* 2.7 44.6 + - - -
142K TRP* 3.7 0.4 - - - -
143K THR* 3.3 10.2 + - - -
----------------------------------------------------------
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