Contacts of the helix formed by residues 64 - 74 (chain A) in PDB entry 1MWT
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 GLU 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS* 4.9 10.3 + - - +
60A VAL* 2.8 51.5 + - + +
63A THR* 1.3 80.2 + - - +
65A ARG* 1.3 65.2 + - - +
66A PRO 3.2 1.6 - - - -
67A ILE* 3.0 26.9 + - + +
68A LYS* 3.4 18.6 + - - +
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Residues in contact with ARG 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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60A VAL* 2.9 10.6 + - + +
61A GLU* 2.7 58.8 + - - +
64A GLU* 1.3 73.2 - - - +
66A PRO* 1.3 71.4 - - + +
68A LYS* 3.2 17.2 + - + +
69A ILE* 3.1 46.5 + - + +
129A HIS* 3.7 14.0 + - - -
132A ILE* 5.1 2.9 - - - -
136A MET* 5.1 4.0 - - - +
139A ASP* 5.6 2.2 - - - +
140A GLN 2.7 30.1 + - - +
141A SER* 3.7 15.8 - - - +
142A ILE 5.1 0.2 - - - +
305B ASN* 5.6 2.1 + - - +
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Residues in contact with PRO 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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42A PHE* 3.7 29.8 - - + -
61A GLU 3.4 8.5 - - - +
62A MET 3.3 19.5 - - - +
63A THR 3.5 9.6 - - - +
64A GLU 3.4 3.6 - - - -
65A ARG* 1.3 94.6 - - + +
67A ILE* 1.3 55.6 + - - +
69A ILE* 4.0 0.6 - - + +
70A TYR* 3.0 37.0 + - + -
132A ILE* 3.4 41.5 - - + -
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Residues in contact with ILE 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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42A PHE* 3.6 22.0 - - + -
63A THR 3.6 20.0 - - - +
64A GLU* 3.0 14.0 + - + +
66A PRO* 1.3 74.5 - - - +
68A LYS* 1.3 61.5 + - + +
70A TYR* 3.4 3.9 + - - +
71A ASN* 2.9 33.4 + - + +
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Residues in contact with LYS 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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60A VAL* 6.2 2.7 - - - -
64A GLU* 3.4 23.3 + - - +
65A ARG* 3.2 14.9 + - + +
67A ILE* 1.3 78.8 - - + +
69A ILE* 1.3 64.6 + - - +
71A ASN* 3.3 8.2 + - - +
72A SER* 3.1 23.0 + - - -
139B ASP* 6.1 3.2 - - - -
305B ASN* 3.3 33.7 - - - +
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Residues in contact with ILE 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 ARG* 3.1 50.4 + - + +
66A PRO* 4.0 3.8 - - + +
68A LYS* 1.3 75.9 - - - +
70A TYR* 1.3 68.3 + - + +
72A SER* 2.9 22.2 + - - +
73A LEU* 3.2 20.5 + - + +
132A ILE* 4.1 21.3 - - + -
133A ILE* 4.5 7.9 - - + -
136A MET* 4.6 11.0 - - + -
142A ILE* 3.9 26.5 - - + -
305B ASN* 3.7 16.2 - - - +
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Residues in contact with TYR 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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37A ILE* 5.3 1.3 + - - +
40A LYS* 4.4 8.7 - - + -
42A PHE* 3.7 32.7 - + - -
66A PRO* 3.0 21.2 + - + +
67A ILE* 3.9 3.8 - - - +
69A ILE* 1.3 82.6 - - + +
71A ASN* 1.3 58.1 + - - +
73A LEU* 3.4 0.4 + - + -
74A GLY* 3.0 23.0 + - - -
75A VAL* 3.2 49.2 + - + +
78A ILE* 3.7 21.0 - - + +
99A TYR* 3.0 17.7 + - - -
101A ILE* 4.5 3.5 - - + +
131A VAL 4.1 1.0 + - - -
132A ILE* 2.7 42.7 + - + -
133A ILE* 3.8 13.9 - - + -
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Residues in contact with ASN 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 ILE* 2.9 23.2 + - + +
68A LYS* 3.7 7.3 + - - +
69A ILE 3.3 0.2 - - - -
70A TYR* 1.3 77.4 - - - +
72A SER* 1.3 63.6 + - - +
74A GLY* 3.6 9.9 + - - +
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Residues in contact with SER 72 (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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68A LYS 3.1 11.9 + - - -
69A ILE* 2.9 18.5 + - - +
71A ASN* 1.3 81.8 - - - +
73A LEU* 1.3 63.7 + - - +
74A GLY 3.7 0.2 + - - -
104A ASN* 5.8 0.2 + - - -
105A TYR* 3.6 16.6 + - - -
142A ILE* 5.8 2.9 - - - +
144A ILE* 4.1 10.3 - - - +
305B ASN* 3.5 36.5 + - - -
306B SER* 4.3 4.9 - - - +
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Residues in contact with LEU 73 (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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69A ILE* 3.2 23.5 + - + +
70A TYR* 5.2 0.2 - - + -
72A SER* 1.3 83.9 + - - +
74A GLY* 1.3 62.7 + - - +
75A VAL* 4.0 19.3 - - + -
101A ILE* 6.0 0.2 - - + -
103A THR* 3.1 18.5 - - + +
104A ASN* 3.1 19.3 + - - +
105A TYR* 3.6 18.6 - - + -
108A ILE* 5.0 8.3 - - + -
133A ILE* 4.2 24.2 - - + -
142A ILE* 4.2 13.7 - - + -
144A ILE* 3.9 18.4 - - + -
299A VAL* 3.8 27.6 - - + -
313A LEU* 5.6 0.9 - - + -
314A ILE* 6.2 0.9 - - + -
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Residues in contact with GLY 74 (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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70A TYR 3.0 6.8 + - - -
71A ASN* 3.6 7.9 + - - -
72A SER 3.3 3.4 - - - -
73A LEU* 1.3 79.1 - - - +
75A VAL* 1.3 61.3 + - - +
76A LYS* 2.9 26.6 - - - +
103A THR* 3.4 0.6 - - - -
104A ASN* 3.3 29.7 + - - -
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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