Contacts of the helix formed by residues 86 - 99 (chain A) in PDB entry 1MD9
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.8 21.1 - - + +
46A CYS* 4.0 16.8 - - + +
49A THR* 2.9 39.9 + - - +
51A TRP* 3.0 79.3 - - + +
85A ILE* 1.3 72.2 - - - +
87A GLU* 1.3 76.2 + - - +
89A PHE* 3.0 23.4 + - - +
255A LEU* 3.5 0.6 - - - +
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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
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51A TRP* 4.0 3.4 - - - -
59A ARG* 5.8 1.2 + - - +
82A LEU* 4.4 5.2 - - + -
85A ILE* 3.1 35.3 - - + +
86A LYS* 1.3 85.7 + - - +
88A PHE* 1.3 65.0 + - - +
89A PHE 2.8 1.0 + - - -
90A GLU* 3.1 24.4 + - - +
91A VAL* 2.7 28.2 + - - +
157A ALA* 4.2 8.3 - - + +
166A LEU* 3.7 28.5 - - + -
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 4.8 8.1 - - + -
82A LEU* 3.8 34.7 - - + +
83A PRO 4.4 5.4 - - - +
85A ILE* 3.5 6.6 + - - +
87A GLU* 1.3 76.8 - - - +
89A PHE* 1.3 70.7 + + - +
91A VAL* 3.8 2.1 - - - +
92A ILE* 3.0 56.5 + - + +
104A PHE* 3.4 39.0 - + - -
232A MSE 3.3 37.0 - - + -
233A ALA* 3.9 22.4 - - + -
238A LEU* 3.9 21.8 - - + -
243A VAL* 4.8 1.6 - - + -
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Residues in contact with PHE 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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44A ILE* 3.2 39.9 - - + -
56A LEU* 3.8 13.5 - - + -
85A ILE 3.7 7.4 - - - -
86A LYS* 3.0 13.9 + - - +
87A GLU 2.8 1.6 + - - -
88A PHE* 1.3 80.6 - + - +
90A GLU* 1.3 69.1 + - - +
91A VAL 3.0 0.7 - - - -
92A ILE* 3.0 17.3 + - + +
93A PHE* 3.1 21.2 + + + -
232A MSE 3.4 35.2 - - + -
243A VAL* 3.9 28.9 - - + -
244A LEU* 4.8 4.7 - - + -
247A LEU* 4.7 21.5 - - + -
253A VAL* 4.6 4.0 - - + -
255A LEU* 3.9 16.4 - - + -
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Residues in contact with GLU 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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51A TRP* 3.7 19.7 - - + -
56A LEU* 3.7 11.8 - - + +
59A ARG* 3.2 35.3 + - + +
60A ALA* 4.2 7.9 - - - +
63A LEU* 3.9 12.0 - - + +
86A LYS 3.6 1.2 + - - -
87A GLU* 3.1 40.2 + - - +
89A PHE* 1.3 76.9 - - - +
91A VAL* 1.3 70.9 + - + +
93A PHE 3.5 0.2 + - - -
94A ALA* 2.9 34.1 + - - +
166A LEU* 4.4 3.2 - - - +
170A HIS* 2.5 37.4 + - - -
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Residues in contact with VAL 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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63A LEU* 3.7 20.0 - - + -
67A PHE* 4.0 1.3 - - + -
80A VAL* 4.2 20.6 - - + -
82A LEU* 4.3 5.4 - - + -
87A GLU 2.7 28.7 + - - +
88A PHE* 3.8 3.6 - - - +
89A PHE 3.0 0.2 + - - -
90A GLU* 1.3 75.9 - - + +
92A ILE* 1.3 65.7 + - + +
94A ALA* 3.6 2.3 - - - +
95A LEU* 3.2 30.6 + - + +
127A ILE* 3.6 30.1 - - + -
166A LEU* 4.0 25.6 - - + -
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Residues in contact with ILE 92 (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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80A VAL* 4.7 6.3 - - + -
88A PHE* 3.0 50.3 + - + +
89A PHE* 3.0 14.4 + - + +
91A VAL* 1.3 79.2 - - + +
93A PHE* 1.3 69.5 + - + +
95A LEU* 3.3 6.0 + - - +
96A PHE* 2.9 55.6 + - + -
102A PRO* 4.2 12.1 - - + -
104A PHE* 4.0 27.8 - - + -
244A LEU* 4.4 18.6 - - + -
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Residues in contact with PHE 93 (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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27A PHE* 3.5 42.6 - + + -
28A GLY* 5.5 0.4 - - - -
30A LEU* 5.2 7.6 - - + -
31A LEU* 3.3 42.8 - - + -
56A LEU* 4.8 6.7 - - + -
60A ALA* 4.2 6.5 - - + -
89A PHE* 3.1 27.5 + + - +
90A GLU* 5.2 0.4 - - - -
92A ILE* 1.3 82.7 - - + +
94A ALA* 1.3 60.6 + - - +
96A PHE* 3.3 12.6 + + - +
97A ARG* 2.9 36.2 + - + +
244A LEU* 4.2 19.3 - - + -
247A LEU* 3.6 32.8 - - + -
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Residues in contact with ALA 94 (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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60A ALA* 3.5 27.5 - - - +
63A LEU* 3.7 21.5 - - + -
64A ALA* 3.7 15.6 - - - +
67A PHE* 4.4 4.0 - - + -
90A GLU 2.9 18.3 + - - +
91A VAL 3.6 5.4 - - - +
93A PHE* 1.3 78.2 - - - +
95A LEU* 1.3 62.1 + - - +
97A ARG* 3.2 2.1 + - - -
98A LEU* 3.0 23.1 + - - +
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Residues in contact with LEU 95 (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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67A PHE* 3.7 24.9 - - + -
72A ILE* 4.5 4.3 - - + -
78A VAL* 3.5 26.7 - - + -
80A VAL* 4.1 20.2 - - + -
91A VAL* 3.2 23.6 + - + +
92A ILE 3.7 4.9 - - - +
93A PHE 3.3 0.2 - - - -
94A ALA* 1.3 79.5 - - - +
96A PHE* 1.3 52.4 + - - +
98A LEU* 3.1 4.5 + - + -
99A GLY 2.7 31.2 + - - -
100A ALA* 2.8 41.5 + - + +
102A PRO* 3.6 28.9 - - + -
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Residues in contact with PHE 96 (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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26A THR* 5.9 0.7 - - - -
27A PHE* 3.4 50.9 - + + -
28A GLY* 5.0 4.6 + - - +
92A ILE* 2.9 48.2 + - + +
93A PHE* 3.4 21.3 - + + +
95A LEU* 1.3 77.0 - - - +
97A ARG* 1.3 62.0 + - + +
99A GLY* 3.5 7.0 + - - -
100A ALA 4.4 2.0 - - - -
102A PRO* 3.5 22.2 - - + -
104A PHE* 4.7 4.0 - + - -
179A VAL* 3.5 19.4 - - - +
185A ALA* 3.4 28.9 - - + -
186A PHE* 4.1 20.2 - + + -
204A HIS* 4.5 7.4 - + + -
244A LEU* 5.3 5.2 - - + -
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Residues in contact with ARG 97 (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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28A GLY* 3.2 40.9 + - - -
31A LEU* 3.8 11.4 - - + +
32A ARG* 3.0 34.9 - - - +
57A ASP* 2.4 46.5 + - - +
60A ALA* 3.6 12.5 - - - +
61A ASP* 3.1 18.3 + - - +
64A ALA* 4.6 10.1 - - + -
93A PHE* 2.9 21.7 + - + +
94A ALA* 3.8 5.4 - - - +
95A LEU 3.2 0.2 - - - -
96A PHE* 1.3 76.3 - - - +
98A LEU* 1.3 63.0 + - - +
99A GLY 3.2 0.4 + - - -
176A LEU* 3.7 25.0 - - + +
177A PRO 4.0 3.8 - - - +
179A VAL* 3.9 10.0 - - - +
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Residues in contact with LEU 98 (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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64A ALA* 4.4 6.5 - - + +
67A PHE* 3.9 21.3 - - + -
68A GLN* 4.0 34.1 - - + +
72A ILE* 3.3 49.4 - - + +
73A GLN* 4.7 2.7 - - - -
74A GLN* 3.8 17.7 + - - +
94A ALA 3.0 15.8 + - - +
95A LEU* 3.1 6.7 + - - +
97A ARG* 1.3 78.0 - - - +
99A GLY* 1.3 58.6 + - - +
100A ALA* 4.1 9.0 - - + +
176A LEU* 4.3 11.0 - - + +
177A PRO* 4.2 12.3 - - + +
179A VAL* 4.5 0.9 - - - -
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Residues in contact with GLY 99 (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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74A GLN* 4.0 9.7 - - - +
75A LYS* 2.8 23.3 + - - +
95A LEU 2.7 4.7 + - - -
96A PHE 3.5 3.5 + - - -
97A ARG 3.2 3.6 - - - -
98A LEU* 1.3 79.9 - - - +
100A ALA* 1.3 65.3 + - - +
101A LEU* 3.5 10.3 - - - +
179A VAL* 3.7 22.2 - - - -
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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
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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