Contacts of the helix formed by residues 69 - 89 (chain B) in PDB entry 3MDS
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 ILE 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA* 3.5 32.8 - - + +
44B LEU* 4.0 19.5 - - + -
46B LYS* 3.9 12.8 - - + +
47B TYR* 3.8 30.3 - - + -
50B LEU* 4.0 12.8 - - + -
65B LEU* 4.4 5.8 - - + -
66B PRO* 3.1 22.9 + - + +
68B ASP* 1.3 82.5 - - - +
70B GLN* 1.3 58.7 + - - +
71B THR 3.3 3.1 - - - -
72B ALA* 3.3 7.1 + - + -
73B VAL* 2.8 50.2 + - + +
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.2 37.3 - - + +
63B ALA* 3.6 20.2 + - - +
65B LEU* 2.9 30.4 + - + +
66B PRO 3.4 4.7 + - - +
67B GLN* 3.7 22.6 + - - +
69B ILE* 1.3 75.9 - - - +
71B THR* 1.3 59.5 + - - +
73B VAL* 4.8 0.4 - - - -
74B ARG* 2.9 29.7 + - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN 5.0 1.6 + - - -
68B ASP 5.5 0.4 + - - -
69B ILE 3.3 0.4 - - - -
70B GLN* 1.3 76.3 - - - +
72B ALA* 1.3 62.0 + - - +
74B ARG* 4.2 9.2 - - + +
75B ASN* 2.9 52.9 + - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN 5.2 1.3 - - - +
40B LEU* 5.2 0.9 - - - +
43B ALA* 3.9 23.3 - - + -
68B ASP 5.1 3.1 + - - +
69B ILE* 3.3 13.2 + - + +
71B THR* 1.3 77.3 - - - +
73B VAL* 1.3 58.1 + - - +
75B ASN* 4.9 1.3 - - - +
76B ASN* 2.9 47.9 + - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.4 21.5 - - + -
43B ALA* 4.5 7.4 - - + -
44B LEU* 4.6 7.0 - - + -
55B VAL* 5.6 0.4 - - + -
58B LEU* 4.1 19.1 - - + -
59B LEU* 3.6 6.3 - - + +
62B LEU* 4.1 7.2 - - + -
65B LEU* 3.8 23.3 - - + -
69B ILE* 2.8 44.7 + - + +
70B GLN 4.0 2.5 - - - +
72B ALA* 1.3 74.9 - - - +
74B ARG* 1.3 60.4 + - - +
77B GLY* 2.7 34.9 + - - +
78B GLY 3.5 0.7 + - - -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.0 6.3 - - - +
62B LEU* 3.8 29.7 - - + +
70B GLN 2.9 18.5 + - - +
71B THR* 3.6 10.5 - - - +
73B VAL* 1.3 76.7 - - - +
75B ASN* 1.3 66.1 + - - +
78B GLY* 3.0 24.6 + - - -
149B PRO* 5.2 2.6 - - - +
151B GLN 4.1 5.7 - - - +
152B ASP* 2.8 42.6 + - - +
156B MET* 4.0 15.8 - - + +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.4 58.5 - - + +
36B TYR* 4.4 0.7 - - - -
71B THR* 2.9 40.0 + - - +
72B ALA* 4.3 1.3 - - - +
74B ARG* 1.3 91.0 + - - +
76B ASN* 1.3 63.5 + - - +
79B GLY* 2.9 20.8 + - - -
150B ASN* 5.3 2.1 - - - +
151B GLN* 3.3 14.9 + - - +
152B ASP* 4.9 2.9 - - - +
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Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 5.0 3.3 - - - -
36B TYR* 3.3 45.2 - - - +
39B ASN* 3.4 35.5 + - - +
40B LEU* 3.7 11.4 - - - +
72B ALA* 2.9 40.0 + - - +
75B ASN* 1.3 76.2 - - - +
77B GLY* 1.3 60.2 + - - +
79B GLY 4.2 0.4 - - - +
80B HIS* 2.9 28.6 + - - +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.9 15.9 - - - +
55B VAL* 3.8 24.6 - - - +
59B LEU* 4.1 3.8 - - - -
73B VAL* 2.7 23.3 + - - -
76B ASN* 1.3 70.1 - - - +
78B GLY* 1.3 62.2 + - - -
80B HIS* 3.4 2.9 + - - +
81B LEU* 3.0 25.6 + - - +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.9 16.5 - - - +
73B VAL 3.5 1.2 + - - -
74B ARG 3.0 16.9 + - - -
77B GLY* 1.3 75.6 - - - +
79B GLY* 1.3 55.2 + - - +
81B LEU* 3.9 0.4 - - - -
82B ASN* 2.9 37.2 + - - +
151B GLN 3.2 23.3 - - - -
153B ASN* 4.7 2.7 - - - -
156B MET* 6.4 0.2 - - - -
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 3.7 18.1 - - - -
75B ASN 2.9 19.7 + - - -
76B ASN 3.4 1.1 + - - -
77B GLY 3.2 0.4 - - - -
78B GLY* 1.3 73.9 - - - +
80B HIS* 1.3 62.2 + - - +
83B HIS* 2.8 32.7 + - - +
151B GLN* 3.5 21.4 - - - +
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Residues in contact with HIS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.1 22.9 - + + +
5B LYS 3.3 26.8 + - - -
7B PRO* 4.2 2.0 - - + -
33B HIS* 3.0 31.9 + - - +
36B TYR* 3.9 3.0 - - + +
37B VAL* 3.5 14.4 - - + +
40B LEU* 4.0 22.9 - - + -
55B VAL* 4.4 13.4 - - + +
76B ASN 2.9 17.3 + - - +
77B GLY 3.5 4.0 - - - +
79B GLY* 1.3 77.5 - - - +
81B LEU* 1.3 63.1 + - - +
84B SER* 2.8 46.1 + - - -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.3 10.8 - - + -
56B GLU* 3.8 41.7 - - + +
59B LEU* 3.9 22.0 - - + -
77B GLY 3.0 16.0 + - - +
78B GLY 4.0 2.5 - - - +
80B HIS* 1.3 78.8 - - - +
82B ASN* 1.3 62.2 + - - +
84B SER* 3.4 6.2 + - - -
85B LEU* 3.2 42.6 + - + +
153B ASN* 3.6 25.1 - - - +
155B VAL* 4.1 8.3 - - + -
161B PRO* 6.1 0.4 - - + -
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY 2.9 19.2 + - - +
79B GLY 4.0 0.4 - - - +
81B LEU* 1.3 72.1 - - - +
83B HIS* 1.3 59.3 + - - +
85B LEU* 3.4 4.1 + - - +
86B PHE* 3.1 26.0 + - - +
132B TRP* 3.5 33.9 - - + +
134B TRP* 3.4 17.1 - - + -
151B GLN* 3.1 44.9 + - - +
152B ASP 3.6 6.5 + - - -
153B ASN* 2.7 36.4 + - - +
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.1 20.0 + + - -
33B HIS* 3.5 28.3 - + + +
36B TYR* 3.5 26.6 - + - -
79B GLY* 2.8 26.0 + - - +
82B ASN* 1.3 79.4 - - - +
84B SER* 1.3 65.7 + - - +
86B PHE* 3.1 6.4 + + - +
87B TRP* 3.0 42.8 + + - +
132B TRP* 3.7 8.5 - + - -
151B GLN* 3.5 18.6 + - - -
166B ASP* 3.2 2.6 + - - -
204B MN3 2.1 37.0 + - - -
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 3.8 10.3 - - - +
33B HIS* 3.3 16.4 - - - -
80B HIS* 2.8 38.0 + - - -
81B LEU* 3.8 8.7 - - - -
83B HIS* 1.3 76.6 - - - +
85B LEU* 1.3 61.6 + - - +
87B TRP* 3.7 6.5 + - - +
88B ARG* 3.4 25.9 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.2 29.0 + - + +
82B ASN 3.7 4.0 - - - +
84B SER* 1.3 76.7 - - - +
86B PHE* 1.3 63.3 + - - +
88B ARG* 3.2 4.4 + - - +
89B LEU* 3.0 33.3 + - + +
132B TRP* 6.3 0.4 - - + -
134B TRP* 4.0 15.5 - - + -
153B ASN* 3.8 13.9 - - - +
161B PRO* 3.8 34.3 - - + +
162B ILE 6.4 0.2 - - - -
164B GLY* 6.0 0.7 - - - +
199B PHE* 3.8 37.1 - - + -
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 5.3 2.9 - - + -
25B MET* 6.2 0.4 - - - -
28B HIS* 4.0 17.3 - + - -
82B ASN 3.1 14.6 + - - +
83B HIS* 3.1 9.6 + + - +
85B LEU* 1.3 77.3 - - - +
87B TRP* 1.3 83.9 + + - +
89B LEU* 3.1 18.2 + - + +
90B LEU* 3.1 45.7 + - + +
132B TRP* 3.7 18.4 - + + -
164B GLY* 3.5 23.3 - - - -
165B ILE* 4.2 3.4 - - + -
166B ASP* 3.9 21.1 - - + -
171B ALA* 5.4 0.2 - - + -
183B TYR* 3.6 22.2 - - - -
187B ILE* 4.1 13.0 - - + -
191B LEU* 5.7 2.2 - - + -
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Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 4.4 9.6 - - + -
8B ASP 5.3 1.3 - - - +
9B LEU* 3.5 34.8 - - + +
11B TYR* 2.8 29.8 + - - -
25B MET* 3.8 22.7 - - + -
28B HIS* 3.7 42.0 - + + -
29B HIS* 3.5 38.0 - + + -
33B HIS* 2.9 29.4 + + - -
83B HIS* 3.0 33.2 + + + +
84B SER* 4.2 6.5 - - - +
86B PHE* 1.3 93.1 - + - +
88B ARG* 1.3 64.6 + - + +
90B LEU* 3.3 6.1 + - + -
91B THR 3.5 0.2 + - - -
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 3.4 15.9 + - - +
85B LEU 3.2 6.8 + - - +
86B PHE 3.2 0.6 - - - -
87B TRP* 1.3 79.8 - - + +
89B LEU* 1.3 59.8 + - - +
91B THR* 2.9 29.1 + - - +
195B VAL* 3.6 29.7 - - + +
198B GLU* 2.9 35.8 + - - -
199B PHE* 3.8 32.7 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.0 25.8 + - + +
86B PHE* 3.1 10.4 + - + +
88B ARG* 1.3 75.0 - - - +
90B LEU* 1.3 58.7 + - + +
91B THR 3.4 1.3 - - - -
162B ILE 3.7 17.3 - - - +
163B VAL* 3.8 10.5 - - + -
164B GLY* 3.5 37.2 - - - +
191B LEU* 3.6 19.6 - - + -
192B ASN* 2.8 34.8 + - - +
195B VAL* 4.1 3.4 - - + -
196B ALA* 4.0 26.2 - - + +
199B PHE* 3.9 16.8 - - + -
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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
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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