Contacts of the helix formed by residues 58 - 72 (chain B) in PDB entry 1MHQ
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 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 5.8 0.7 - - - -
56B ASP* 2.7 24.9 + - - +
57B PRO* 1.3 92.3 + - - +
59B GLY* 1.3 66.3 + - - +
60B PRO 3.3 2.9 - - - -
61B THR* 2.6 34.9 + - - +
62B HIS* 3.0 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.0 17.3 - - - -
53B VAL* 4.0 11.4 - - - -
56B ASP* 3.1 20.8 + - - -
58B ASN* 1.3 79.1 - - - +
60B PRO* 1.3 63.5 - - - +
61B THR 3.1 0.2 + - - -
63B ALA* 3.0 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.3 31.2 - - + +
56B ASP 3.5 7.6 - - - +
57B PRO* 4.1 7.9 - - + +
58B ASN 3.6 2.0 - - - -
59B GLY* 1.3 87.4 - - - +
61B THR* 1.3 58.8 + - + +
62B HIS 3.5 0.2 - - - -
63B ALA* 5.0 0.2 - - + -
64B PRO* 3.6 9.9 - - + +
96B LYS* 3.9 38.6 - - + +
97B PHE* 4.9 5.2 - - + +
100B GLU* 2.9 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO 4.0 8.1 - - - +
58B ASN* 2.6 41.4 + - + +
60B PRO* 1.3 83.8 - - + +
62B HIS* 1.3 70.1 + - - +
64B PRO* 4.2 0.2 - - - -
65B TRP* 3.1 24.8 + - - +
100B GLU* 4.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.6 10.5 - - + -
58B ASN* 3.0 22.2 + - + +
59B GLY 4.3 0.4 - - - +
61B THR* 1.3 99.6 + - - +
63B ALA* 1.3 65.7 - - - +
64B PRO* 3.4 3.1 - - - -
65B TRP* 3.0 21.1 + - - +
66B LEU* 3.2 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.8 19.5 - - + +
49B PHE* 3.8 18.0 - - + -
53B VAL* 4.1 13.2 - - + -
59B GLY 3.0 18.1 + - - +
62B HIS* 1.3 76.1 - - - +
64B PRO* 1.3 62.9 - - + +
65B TRP 3.1 0.3 + - - -
66B LEU* 3.1 7.5 + - - +
67B LEU* 2.7 34.6 + - + +
97B PHE* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO 3.6 24.0 - - - +
61B THR 4.4 0.2 - - - +
62B HIS 3.4 1.6 - - - -
63B ALA* 1.3 94.3 - - + +
65B TRP* 1.3 83.6 + - + +
67B LEU* 4.2 7.2 - - + -
68B ALA* 2.8 28.9 + - - +
97B PHE* 4.6 13.6 - - + -
100B GLU* 4.1 15.7 - - + -
101B VAL* 5.0 3.1 - - + -
106B PHE* 3.3 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 4.3 7.3 - - + +
122A TRP* 3.9 27.3 - + + -
61B THR* 3.1 28.6 + - - +
62B HIS* 3.0 11.9 + - - +
64B PRO* 1.3 90.7 - - + +
66B LEU* 1.3 68.4 + - + +
67B LEU 3.1 1.3 - - - -
68B ALA* 3.2 6.3 + - + +
69B HIS* 3.2 22.7 + - - +
100B GLU* 5.1 13.5 - - + +
103B LYS* 6.1 2.7 - - + -
105B ARG* 3.2 74.4 - - + +
106B PHE* 3.5 35.9 - + + -
109B GLU* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 4.0 26.8 - - + +
75A GLN* 4.3 9.6 + - + +
26B LEU* 3.9 30.1 - - + -
27B GLU* 4.1 34.1 - - + +
30B LEU* 3.6 23.8 - - + +
49B PHE* 5.0 0.2 - - + -
62B HIS* 3.2 32.6 + - + +
63B ALA* 3.1 7.2 + - - +
65B TRP* 1.3 78.1 - - + +
67B LEU* 1.3 62.2 + - - +
69B HIS* 3.6 3.6 + - - +
70B LYS* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.0 17.2 - - + +
49B PHE* 4.4 15.0 - - + -
63B ALA 2.7 16.9 + - - +
64B PRO* 3.6 5.2 - - + +
66B LEU* 1.3 76.4 - - - +
68B ALA* 1.3 63.9 + - - +
70B LYS* 3.1 4.9 + - - +
71B ILE* 2.9 38.4 + - + +
82B ALA* 3.5 28.5 - - + +
85B VAL* 3.7 19.5 - - + -
86B LEU* 4.1 19.3 - - + -
89B CYS* 5.0 0.7 - - - -
97B PHE* 4.1 27.6 - - + -
106B PHE* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TRP* 4.4 4.7 - - + -
64B PRO 2.8 21.9 + - - +
65B TRP* 3.6 10.1 - - + +
67B LEU* 1.3 74.4 - - - +
69B HIS* 1.3 62.0 + - - +
71B ILE* 3.0 16.9 + - - +
72B GLN* 3.1 21.4 + - - +
106B PHE* 4.1 13.2 - - + -
109B GLU* 3.8 33.8 - - + +
110B LEU* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 2.8 82.0 + + - -
72A GLN* 3.9 9.2 - - + -
73A SER* 3.4 32.1 + - - -
74A PRO* 3.3 26.0 - - + +
75A GLN* 5.7 1.4 + - - -
78A GLU* 4.3 12.1 + - - -
122A TRP* 3.8 10.2 - + + -
65B TRP 3.2 10.2 + - - +
66B LEU 3.9 2.9 + - - +
67B LEU 3.3 0.2 - - - -
68B ALA* 1.3 78.3 - - - +
70B LYS* 1.3 76.2 + - + +
72B GLN* 2.9 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 4.8 2.9 - - - -
75A GLN* 3.5 11.2 - - - +
78A GLU* 4.5 13.3 + - - -
30B LEU* 4.2 9.9 - - + -
31B ASN* 2.6 31.5 + - - +
34B THR* 3.2 39.5 - - + +
66B LEU 3.3 14.9 + - - +
67B LEU* 3.1 13.6 + - + +
69B HIS* 1.3 89.5 + - - +
71B ILE* 1.3 61.9 + - - +
73B SER* 3.3 18.4 + - - -
78B GLU* 3.3 25.2 + - + +
79B ALA* 3.5 10.6 - - - -
82B ALA* 3.6 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 2.9 32.8 + - + +
68B ALA* 3.0 11.6 + - - +
70B LYS* 1.3 77.3 - - - +
72B GLN* 1.3 59.9 + - + +
73B SER 3.2 1.9 + - - +
79B ALA* 3.6 15.0 - - - +
82B ALA* 3.7 18.4 - - + -
83B LEU* 3.8 37.0 - - + +
86B LEU* 4.2 20.0 - - + -
106B PHE* 4.6 4.5 - - + -
110B LEU* 4.5 16.8 - - + -
113B VAL* 4.0 25.5 - - + +
123B ALA* 5.7 0.7 - - - +
127B VAL* 4.5 1.6 - - + +
131B VAL* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 3.7 8.5 - - + +
72A GLN* 5.8 0.2 - - - +
122A TRP* 4.6 6.8 - - - -
68B ALA 3.1 15.3 - - - +
69B HIS* 2.9 19.4 + - - +
71B ILE* 1.3 78.8 - - - +
73B SER* 1.3 63.8 + - - +
109B GLU* 2.4 56.2 + - + +
112B LYS* 3.9 12.9 + - + +
113B VAL* 3.6 23.1 - - + +
122B TRP* 3.5 28.9 - - + +
123B ALA* 6.4 1.6 - - - -
----------------------------------------------------------
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