Contacts of the helix formed by residues 75 - 91 (chain A) in PDB entry 5H5Q
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 LYS 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A OCS 2.6 20.6 + - - +
74A GLY* 1.3 73.5 - - - +
76A THR* 1.3 63.8 + - - +
77A GLU 3.3 2.5 - - - -
78A VAL* 3.2 17.7 - - + +
79A ASN* 2.9 37.4 + - - +
165A PHE* 4.5 2.7 - - + -
182A PRO* 4.1 21.3 - - + +
183A MET* 4.8 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 2.8 27.8 + - - +
71A SER 3.4 16.7 - - - +
73A OCS 3.0 34.0 + - - +
74A GLY 3.4 0.4 - - - -
75A LYS* 1.3 77.0 - - - +
77A GLU* 1.3 59.1 + - - +
79A ASN* 3.8 0.3 - - - +
80A TYR* 2.9 37.5 + - + +
119A PHE* 3.6 25.8 - - + -
123A TYR* 4.8 1.3 - - + +
165A PHE* 3.8 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A OCS 4.8 0.2 + - - -
74A GLY 4.8 4.1 + - - +
75A LYS* 3.3 0.6 - - - +
76A THR* 1.3 80.4 - - - +
78A VAL* 1.3 60.8 + - - +
81A THR* 2.9 39.6 + - + +
123A TYR* 3.5 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY 5.5 0.2 + - - -
75A LYS* 3.2 34.9 - - + +
77A GLU* 1.3 79.3 - - - +
79A ASN* 1.3 70.7 + - - +
81A THR* 3.3 5.0 + - - +
82A GLN* 3.0 52.1 + - + +
185A GLU* 4.5 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 2.9 42.3 + - - +
76A THR 3.9 0.2 - - - +
78A VAL* 1.3 84.2 - - - +
80A TYR* 1.3 63.5 + - - +
83A LEU* 2.9 32.2 + - + +
165A PHE* 3.4 39.6 - - + +
167A LYS* 2.9 36.7 + - - +
182A PRO 4.7 4.8 + - - -
185A GLU* 5.6 1.8 - - - +
186A PRO* 3.4 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.4 31.1 - - + +
70A ALA 4.1 10.8 - - - -
71A SER* 5.1 0.3 + - - -
76A THR* 2.9 36.0 + - + +
77A GLU 4.2 1.3 - - - +
79A ASN* 1.3 77.1 - - - +
81A THR* 1.3 63.9 + - - +
83A LEU* 3.3 6.8 + - + +
84A VAL* 3.0 29.5 + - - +
109A GLU* 4.8 1.6 + - - -
116A ILE* 4.7 4.9 - - - +
119A PHE* 4.0 22.6 - + - -
120A ALA* 3.9 22.6 - - + +
123A TYR* 3.9 24.7 - + + -
125A VAL* 3.7 22.9 - - + -
127A PHE* 4.5 9.0 - + - -
129A MET* 3.6 18.1 - - - +
165A PHE* 4.2 12.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 2.9 33.1 + - + +
78A VAL* 3.3 9.2 + - - +
80A TYR* 1.3 76.0 - - - +
82A GLN* 1.3 62.8 + - - +
84A VAL* 3.4 6.6 + - - +
85A ASP* 2.9 36.7 + - - +
123A TYR* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 3.0 37.5 + - + +
81A THR* 1.3 79.3 - - - +
83A LEU* 1.3 60.3 + - - +
85A ASP* 3.3 11.7 + - - +
86A LEU* 2.9 31.9 + - - +
185A GLU* 3.2 38.0 + - - +
186A PRO* 3.2 14.4 - - + -
187A LEU* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.6 13.7 - - + -
67A THR* 4.1 24.2 - - + +
69A VAL* 4.9 8.5 - - + -
79A ASN* 2.9 31.0 + - + +
80A TYR* 3.8 7.0 - - + +
82A GLN* 1.3 71.9 - - - +
84A VAL* 1.3 67.1 + - - +
86A LEU* 3.3 7.6 + - + -
87A HIS* 2.9 19.9 + - - +
97A ILE* 3.4 32.8 - - + +
127A PHE* 3.8 26.0 - - + -
165A PHE* 5.0 2.2 - - + -
167A LYS* 5.3 4.7 - - + -
186A PRO* 3.9 21.8 - - + -
189A ILE* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR 3.0 21.2 + - - +
81A THR* 3.6 7.6 - - - +
83A LEU* 1.3 75.0 - - - +
85A ASP* 1.3 60.0 + - - +
87A HIS* 3.3 4.6 + - - +
88A ALA* 2.8 32.8 + - + +
123A TYR* 3.5 26.9 - - + +
124A ASN* 4.0 12.8 - - + +
125A VAL* 3.8 28.3 - - + -
126A LYS 5.3 0.4 - - - +
127A PHE* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 2.9 27.0 + - - +
82A GLN* 3.3 20.9 + - - +
84A VAL* 1.3 80.2 - - - +
86A LEU* 1.3 62.3 + - - +
88A ALA* 3.3 5.6 + - - +
89A ARG* 3.0 39.5 + - - +
187A LEU* 4.5 17.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
65A ILE* 4.0 24.9 - - + -
82A GLN 2.9 17.8 + - - +
83A LEU* 3.6 11.0 - - + +
85A ASP* 1.3 76.4 - - - +
87A HIS* 1.3 58.3 + - - +
89A ARG* 3.3 1.2 + - - +
90A TYR* 2.9 52.4 + - + +
95A LEU* 3.9 11.2 - - + -
97A ILE* 4.5 1.8 - - + -
186A PRO* 3.5 31.4 - - + +
187A LEU* 3.9 21.3 - - + -
189A ILE* 4.6 3.1 - - + -
190A GLU* 4.0 24.5 - - + +
193A LEU* 4.5 3.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
83A LEU 2.9 17.4 + - - +
84A VAL* 3.7 4.3 - - - +
86A LEU* 1.3 76.4 - - - +
88A ALA* 1.3 63.9 + - - +
91A ALA* 2.9 48.9 + - + +
95A LEU* 4.0 24.9 + - - -
96A ARG* 4.9 7.6 + - - -
97A ILE* 4.0 14.3 - - + +
126A LYS* 3.8 40.7 + - + +
127A PHE* 3.8 26.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 2.8 20.8 + - + +
85A ASP* 3.3 8.5 + - - +
87A HIS* 1.3 79.5 + - - +
89A ARG* 1.3 65.4 + - + +
91A ALA* 4.6 2.1 + - - +
92A GLU* 5.6 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASP* 3.0 24.4 + - - +
86A LEU* 4.5 2.8 - - - +
88A ALA* 1.3 83.5 - - + +
90A TYR* 1.3 81.0 + - + +
92A GLU* 5.3 3.5 + - - +
93A ARG* 4.9 5.4 - - - +
187A LEU* 3.6 19.4 - - - +
190A GLU* 2.6 44.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 2.9 33.0 + - + +
89A ARG* 1.3 99.2 + - + +
91A ALA* 1.3 65.5 + - - +
92A GLU 3.1 3.1 - - - -
93A ARG* 2.9 45.1 + - - +
94A GLY 3.3 0.3 + - - -
95A LEU* 3.2 30.3 + - + -
190A GLU* 2.4 52.3 + - + +
193A LEU* 3.8 17.0 - - + -
194A PRO* 5.5 5.8 - - + +
197A PHE* 3.7 23.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 2.9 47.3 + - + +
88A ALA 4.6 1.5 + - - +
89A ARG 3.9 0.2 - - - -
90A TYR* 1.3 75.7 - - - +
92A GLU* 1.3 62.0 + - + +
94A GLY* 2.9 10.2 + - - -
95A LEU* 3.6 14.9 - - - +
96A ARG* 2.9 25.5 + - - +
----------------------------------------------------------
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