Contacts of the helix formed by residues 53 - 71 (chain A) in PDB entry 1MDF
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 TYR 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.1 12.1 - - + +
34A ARG* 4.0 17.7 - - + -
35A ALA* 3.7 16.6 - - - +
38A TYR* 4.0 22.0 - + + -
39A GLY 3.5 5.4 + - - +
41A ARG* 3.0 32.0 + - - -
42A ILE 4.0 3.6 - - - -
43A ALA* 3.3 33.8 - - + +
52A SER* 1.3 71.4 - - - +
54A ARG* 1.3 57.5 + - - +
56A LEU* 3.2 6.6 + - + +
57A ASP* 2.9 30.0 + - - +
246A VAL 3.5 3.3 + - - -
247A LEU* 3.4 39.0 + - + +
250A GLY* 3.0 19.1 - - - -
251A GLY 2.8 26.7 + - - -
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 3.4 29.4 + - - +
36A ALA* 3.7 22.6 + - - +
39A GLY* 2.9 39.3 + - - +
40A ASP* 5.1 0.2 - - - -
52A SER* 3.8 3.8 - - - +
53A TYR* 1.3 76.8 - - - +
55A GLU* 1.3 60.3 + - - +
57A ASP* 3.5 5.3 + - - +
58A THR* 2.9 33.8 + - - +
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Residues in contact with GLU 55 (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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50A HIS 3.8 3.7 - - - +
51A TRP* 3.2 44.7 + - + -
52A SER* 2.9 24.5 + - - +
54A ARG* 1.3 75.8 - - - +
56A LEU* 1.3 60.4 + - - +
58A THR* 3.4 5.0 + - - -
59A ARG* 2.9 58.9 + - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.7 28.7 - - + -
43A ALA* 5.0 5.2 - - + -
44A ILE* 4.1 22.0 - - + -
51A TRP* 4.5 11.7 - - + -
52A SER 3.0 10.8 + - - +
53A TYR* 3.5 9.9 - - + +
55A GLU* 1.3 74.2 - - - +
57A ASP* 1.3 68.4 + - - +
58A THR 3.2 0.2 + - - -
59A ARG* 3.2 3.7 + - - +
60A ALA* 2.8 26.6 + - + +
89A PHE* 3.9 12.1 - - + +
90A GLU* 3.7 35.7 - - + +
93A PHE* 4.7 1.8 - - + -
247A LEU* 4.2 24.5 - - + -
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.8 16.5 - - + +
32A ARG* 3.4 26.8 + - - +
35A ALA* 3.3 34.7 - - + +
53A TYR 2.9 7.4 + - - +
54A ARG* 3.5 7.7 + - - +
56A LEU* 1.3 78.1 - - - +
58A THR* 1.3 62.6 + - - +
60A ALA* 3.4 0.2 - - - +
61A ASP* 3.2 8.5 + - - +
97A ARG* 2.5 61.0 + - - +
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Residues in contact with THR 58 (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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54A ARG* 2.9 22.5 + - - +
55A GLU* 3.7 5.6 - - - -
57A ASP* 1.3 75.1 + - - +
59A ARG* 1.3 68.3 + - + +
60A ALA 3.0 1.3 - - - -
61A ASP* 2.9 19.1 + - + +
62A ARG* 2.9 31.6 + - + +
173A PRO* 5.8 2.9 - - + -
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Residues in contact with ARG 59 (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* 2.9 43.7 - - - +
55A GLU* 2.9 51.7 + - + +
56A LEU* 3.9 2.9 - - - +
58A THR* 1.3 74.7 - - + +
60A ALA* 1.3 57.3 + - - +
62A ARG* 3.5 5.3 + - - +
63A LEU* 2.8 31.7 + - - +
87A GLU* 4.6 5.3 + - - +
90A GLU* 3.0 46.2 + - + +
170A HIS* 3.8 24.2 + - + +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.2 2.5 - - + -
56A LEU 2.8 17.8 + - - +
57A ASP 3.4 6.5 - - - +
59A ARG* 1.3 77.0 - - - +
61A ASP* 1.3 57.6 + - - +
63A LEU 3.3 0.5 + - - -
64A ALA* 2.9 26.9 + - - +
90A GLU* 4.0 19.0 - - - +
93A PHE* 4.1 26.2 - - + -
94A ALA* 3.4 12.1 - - - +
97A ARG* 3.8 13.0 - - - +
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 2.5 34.2 + - - -
57A ASP* 3.2 6.8 + - - +
58A THR* 2.9 11.3 + - + +
60A ALA* 1.3 75.7 - - - +
62A ARG* 1.3 66.9 + - - +
64A ALA* 3.1 8.2 + - - +
65A ALA* 3.1 21.0 + - - +
97A ARG* 2.8 33.9 + - - +
173A PRO* 4.2 24.5 - - + +
174A VAL 5.1 0.9 + - - -
176A LEU* 5.0 10.2 - - + +
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Residues in contact with ARG 62 (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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58A THR* 2.9 34.0 + - + +
59A ARG* 3.9 7.6 - - - +
61A ASP* 1.3 76.7 - - - +
63A LEU* 1.3 63.7 + - - +
65A ALA* 3.1 11.6 + - - +
66A GLY 3.1 9.5 + - - -
169A LEU 3.4 0.2 - - - +
170A HIS* 4.0 22.4 + - + +
171A THR* 3.2 56.0 + - - +
172A GLU* 3.9 13.1 + - - +
173A PRO* 3.9 23.1 - - + +
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Residues in contact with LEU 63 (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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59A ARG 2.8 19.0 + - - +
60A ALA 3.7 3.6 - - - +
62A ARG* 1.3 76.9 - - - +
64A ALA* 1.3 56.4 + - - +
66A GLY 3.3 0.7 + - - -
67A PHE* 2.9 44.2 + - + -
90A GLU* 3.5 41.3 - - + +
91A VAL* 3.7 21.3 - - + -
94A ALA* 3.7 4.9 - - + -
166A LEU* 3.6 24.2 - - + -
169A LEU* 3.5 30.2 - - + +
170A HIS* 3.8 14.1 - - + +
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Residues in contact with ALA 64 (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 2.9 14.1 + - - +
61A ASP* 3.4 12.3 - - - +
62A ARG 3.1 0.2 - - - -
63A LEU* 1.3 73.9 - - - +
65A ALA* 1.3 59.7 + - - +
67A PHE* 3.2 1.6 + - - -
68A GLN* 2.8 28.6 + - - +
94A ALA* 3.8 16.1 - - - +
97A ARG* 4.6 4.9 - - + -
98A LEU* 3.0 29.0 - - + +
176A LEU* 4.5 17.3 - - + -
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Residues in contact with ALA 65 (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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61A ASP 3.1 11.8 + - - +
62A ARG 3.1 9.2 + - - +
64A ALA* 1.3 77.4 - - - +
66A GLY* 1.3 56.9 + - - +
68A GLN* 3.4 2.9 + - - +
69A LYS* 2.9 30.1 + - - +
171A THR* 3.5 12.8 - - + +
172A GLU 3.3 27.4 - - - +
173A PRO* 4.2 2.0 - - + -
174A VAL* 4.0 26.7 - - + +
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Residues in contact with GLY 66 (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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62A ARG 3.1 7.9 + - - -
65A ALA* 1.3 77.5 - - - +
67A PHE* 1.3 61.3 + - - +
69A LYS* 3.3 6.9 + - - +
70A LEU* 2.8 29.6 + - - +
169A LEU* 3.0 31.6 - - - +
171A THR* 3.7 9.8 - - - +
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Residues in contact with PHE 67 (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* 2.9 35.7 + - + +
64A ALA* 3.6 4.5 - - - +
66A GLY* 1.3 74.6 - - - +
68A GLN* 1.3 66.4 + - - +
70A LEU* 2.9 15.7 + - + +
71A GLY 3.0 10.0 + - - -
72A ILE* 3.2 19.3 + - + +
91A VAL* 4.2 7.2 - - + -
94A ALA* 4.2 13.9 - - + -
95A LEU* 3.8 34.8 - - + -
98A LEU* 4.0 13.9 - - + -
127A ILE* 4.1 15.5 - - + -
155A ILE* 3.5 13.2 - - + -
166A LEU* 3.7 20.6 - - + -
169A LEU* 3.2 34.3 - - + -
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Residues in contact with GLN 68 (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 2.8 19.9 + - - +
65A ALA* 3.6 4.7 - - - +
67A PHE* 1.3 71.5 - - - +
69A LYS* 1.3 58.3 + - - +
71A GLY* 2.9 22.5 + - - -
72A ILE 3.8 15.4 + - - +
98A LEU* 3.8 11.0 - - + +
174A VAL* 3.4 23.4 - - - +
175A LYS 4.3 5.0 + - - +
176A LEU* 3.8 17.5 - - + +
177A PRO* 3.9 21.0 - - - +
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Residues in contact with LYS 69 (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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65A ALA 2.9 16.2 + - - +
66A GLY* 3.4 7.0 - - - +
68A GLN* 1.3 77.3 - - - +
70A LEU* 1.3 63.2 + - - +
71A GLY* 3.3 1.0 + - - -
171A THR* 4.1 29.6 + - + +
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Residues in contact with LEU 70 (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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66A GLY 2.8 16.4 + - - +
67A PHE* 2.9 13.0 + - + +
69A LYS* 1.3 74.7 - - - +
71A GLY* 1.3 58.6 + - - +
72A ILE* 4.9 6.3 - - + +
153A ASN* 4.2 26.4 + - + +
155A ILE* 3.9 23.3 - - + -
164A LEU* 3.6 39.9 - - + -
169A LEU* 4.1 17.9 - - + -
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Residues in contact with GLY 71 (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 3.0 0.2 + - - -
68A GLN 2.9 12.1 + - - -
69A LYS 3.1 1.1 - - - -
70A LEU* 1.3 79.9 - - - +
72A ILE* 1.3 67.8 + - - +
73A GLN* 3.4 14.1 + - - +
76A ASP* 4.1 2.9 - - - +
124A ALA* 6.0 0.5 - - - +
153A ASN* 5.7 4.0 - - - -
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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
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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