Contacts of the helix formed by residues 75 - 93 (chain A) 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 GLN 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.6 13.2 - - + +
73A SER* 2.8 13.9 + - - +
74A PRO* 1.3 80.3 - - + +
76A GLU* 1.3 65.1 - - - +
77A LYS 3.3 1.6 - - - +
78A GLU* 2.9 27.0 + - + +
79A ALA 3.1 8.3 + - - -
27B GLU* 3.5 43.5 - - + +
30B LEU* 5.1 4.4 - - - +
31B ASN* 2.8 44.1 + - - -
66B LEU* 4.3 13.8 + - + +
69B HIS* 5.7 1.6 + - - -
70B LYS* 3.5 15.2 - - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 4.9 0.9 - - - -
74A PRO 3.5 7.3 + - - +
75A GLN* 1.3 71.8 - - - +
77A LYS* 1.3 59.2 + - - +
79A ALA* 3.0 8.5 + - - +
80A LEU* 2.9 54.1 + - + +
124A THR* 2.4 51.3 + - + +
126A LYS* 3.2 24.2 - - - +
127A VAL* 3.9 4.5 - - + -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.2 36.8 - - + +
38A MET 3.8 6.1 - - - +
39A SER* 3.8 13.3 + - - +
75A GLN* 3.3 1.6 - - + -
76A GLU* 1.3 78.9 + - - +
78A GLU* 1.3 63.2 + - - +
80A LEU* 4.2 7.6 - - - -
81A TYR* 3.0 66.0 + - + +
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.9 19.1 - - - +
36A PRO* 4.1 18.1 - - + +
69A HIS* 5.7 0.5 + - - -
70A LYS* 3.6 36.1 + - + +
73A SER* 2.7 33.0 + - - +
75A GLN* 2.9 30.4 + - + +
77A LYS* 1.3 80.6 - - - +
79A ALA* 1.3 62.4 + - - +
81A TYR* 3.7 1.7 - - - +
82A ALA* 3.1 23.2 + - - +
69B HIS* 4.3 9.7 - - - -
70B LYS* 4.5 9.9 + - - -
78B GLU* 5.4 2.1 - - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS 3.4 13.2 + - - +
71A ILE* 3.5 22.0 - - - +
73A SER 4.1 10.1 - - - +
75A GLN 3.1 9.5 + - - +
76A GLU* 3.0 9.7 + - - +
78A GLU* 1.3 74.2 - - - +
80A LEU* 1.3 59.4 + - - +
82A ALA* 3.2 4.2 + - - +
83A LEU* 2.8 34.2 + - - +
123A ALA* 6.3 0.7 - - + -
127A VAL* 3.7 20.2 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 2.9 58.9 + - + +
77A LYS* 3.9 7.0 - - - +
79A ALA* 1.3 74.8 - - - +
81A TYR* 1.3 71.2 + - + +
83A LEU* 3.0 8.6 + - + +
84A THR* 2.9 25.7 + - - -
126A LYS* 4.4 18.2 - - + -
127A VAL* 3.7 28.0 - - + +
130A ARG* 4.2 21.3 + - + +
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA 4.0 4.5 - - - -
34A THR* 3.6 31.6 - - - +
35A ASP 3.2 20.9 - - - -
38A MET* 2.9 21.9 + - + -
39A SER 3.6 1.9 + - - -
40A GLU* 3.4 12.3 - - - -
41A GLN* 3.0 55.9 + - + +
77A LYS* 3.0 51.3 + - + +
78A GLU 3.7 3.8 - - - +
80A LEU* 1.3 81.5 - - + +
82A ALA* 1.3 57.6 + - - +
84A THR* 3.1 3.3 + - - -
85A VAL* 2.9 24.9 + - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.9 12.8 - - + +
67A LEU* 4.0 8.0 - - + +
70A LYS* 3.7 26.9 - - + -
71A ILE* 3.7 16.4 - - + +
78A GLU 3.1 12.2 + - - +
79A ALA 3.4 8.5 - - - +
81A TYR* 1.3 75.4 - - - +
83A LEU* 1.3 56.2 + - - +
85A VAL* 2.9 5.3 + - - +
86A LEU* 2.7 35.9 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.7 32.1 - - + -
79A ALA 2.8 16.5 + - - +
80A LEU* 3.3 14.1 - - + +
82A ALA* 1.3 75.2 - - - +
84A THR* 1.3 57.5 + - - +
86A LEU* 3.2 9.1 + - + +
87A GLU* 2.9 29.1 + - - +
110A LEU* 4.6 2.2 - - + -
127A VAL* 3.8 28.9 - - + +
130A ARG* 3.7 35.0 - - + +
131A VAL* 4.0 12.6 - - + -
134A ILE* 3.7 26.3 - - + +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.7 23.6 + - - +
43A TRP* 4.8 12.3 - - + +
46A ILE* 4.3 10.8 - - + -
80A LEU 2.9 12.6 + - - -
81A TYR* 3.3 8.2 - - - -
83A LEU* 1.3 78.1 - - - +
85A VAL* 1.3 62.7 + - - +
87A GLU* 3.1 5.2 + - + +
88A MET* 2.9 23.8 + - + +
130A ARG* 3.4 20.0 + - - +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.0 3.1 - - + -
33A ALA* 4.0 13.7 - - + -
34A THR* 4.0 18.2 - - + -
41A GLN* 3.7 13.7 - - - +
46A ILE* 4.0 18.4 - - + -
49A PHE* 3.4 39.7 - - + -
67A LEU* 3.7 11.0 - - + -
81A TYR 2.9 20.3 + - - +
82A ALA 2.9 5.8 + - - +
84A THR* 1.3 75.7 - - - +
86A LEU* 1.3 58.4 + - - +
88A MET* 3.2 1.9 + - - +
89A CYS* 2.9 30.3 + - - -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.0 26.9 - - + +
71A ILE* 3.8 24.7 - - + -
82A ALA 2.7 15.4 + - - +
83A LEU* 3.4 15.5 - - + +
85A VAL* 1.3 72.6 - - - +
87A GLU* 1.3 64.8 + - - +
89A CYS* 3.3 1.3 + - - -
90A MET* 3.0 23.5 + - + +
97A PHE* 4.4 12.1 - - + -
101A VAL* 4.4 3.1 - - + -
106A PHE* 4.3 15.3 - - + -
110A LEU* 4.1 16.6 - - + -
134A ILE* 4.7 6.5 - - + -
138A TRP* 4.0 33.0 - - + -
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU 2.9 10.6 + - - +
84A THR* 3.3 11.2 - - + +
86A LEU* 1.3 80.4 - - - +
88A MET* 1.3 62.5 + - - +
90A MET* 3.6 4.4 + - - +
91A ASN* 3.1 34.9 + - - +
130A ARG* 2.4 48.9 + - - -
133A GLU* 4.9 3.1 - - - +
134A ILE* 3.9 16.9 - - + +
138A TRP* 5.6 3.3 + - - +
141A TRP* 5.1 13.0 - - + -
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TRP* 3.5 36.1 - - + -
46A ILE* 3.7 24.9 - - + -
47A GLN* 4.2 24.7 - - + +
50A CYS* 3.9 11.9 - - + -
84A THR* 2.9 17.6 + - + +
85A VAL 3.7 3.4 - - - +
87A GLU* 1.3 75.5 - - - +
89A CYS* 1.3 65.3 + - - +
91A ASN* 3.2 2.5 + - - +
92A HIS* 2.9 59.4 + - + +
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Residues in contact with CYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.4 31.9 - - - -
50A CYS* 2.1 48.8 - - - -
53A VAL* 4.6 1.1 - - - -
67A LEU* 5.0 0.7 - - + -
85A VAL* 2.9 21.1 + - - +
86A LEU* 4.0 2.2 - - - +
88A MET* 1.3 71.7 - - - +
90A MET* 1.3 62.0 + - - +
93A CYS* 2.8 45.5 + - - +
97A PHE* 3.6 20.1 - - + -
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.0 16.0 + - + +
87A GLU 4.0 5.2 - - - +
88A MET 3.3 0.2 - - - -
89A CYS* 1.3 77.1 - - - +
91A ASN* 1.3 65.6 + - - +
93A CYS 4.5 5.7 - - - +
97A PHE* 3.9 9.3 - - + -
98A HIS* 3.3 65.3 + - + +
101A VAL* 3.6 27.8 - - + -
138A TRP* 3.2 51.4 - - + +
142A PHE* 4.2 12.7 - - + -
148A ILE* 4.3 9.2 - - + -
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Residues in contact with ASN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.1 25.2 + - - +
88A MET* 3.2 3.3 + - - +
89A CYS 3.1 0.6 - - - -
90A MET* 1.3 85.0 - - - +
92A HIS* 1.3 81.2 + - + +
93A CYS 4.5 2.0 - - - +
138A TRP* 6.3 0.2 - - - -
141A TRP* 4.0 32.6 - - - -
142A PHE* 4.3 10.0 - - - -
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 4.8 11.4 - - + -
54A ASN* 3.9 10.1 + - - -
88A MET* 2.9 49.8 + - + +
91A ASN* 1.3 95.4 - - + +
93A CYS* 1.3 67.6 + - - +
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Residues in contact with CYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 3.2 42.8 - - - -
53A VAL* 3.8 13.7 - - + -
54A ASN* 3.1 10.5 - - - +
89A CYS* 2.8 36.2 + - - +
90A MET 4.5 6.1 - - - +
91A ASN 4.5 2.1 - - - +
92A HIS* 1.3 78.7 + - - +
94A GLY* 1.3 65.0 + - - +
97A PHE* 3.7 21.3 - - + -
98A HIS* 5.5 1.0 - - - +
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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) + - + + + + + -
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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