Contacts of the helix formed by residues 62 - 72 (chain A) in PDB entry 4M2O
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 PRO 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.5 31.6 - - + +
54A SER* 3.6 20.2 - - - +
57A PHE* 4.1 7.9 - - + +
60A ALA 3.4 9.2 - - - +
61A ASP* 1.3 86.5 - - - +
63A LYS* 1.3 61.5 + - + +
64A ALA 3.4 2.2 - - - -
65A TYR* 3.3 3.1 + - + +
66A ALA* 2.9 30.6 + - - +
132A MET* 3.4 34.1 - - + -
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN 5.4 0.9 - - - -
50A GLN* 3.0 53.7 + - - +
51A THR* 4.2 7.4 + - - +
54A SER* 2.6 40.1 + - - +
61A ASP 3.4 3.6 + - - -
62A PRO* 1.3 79.2 - - + +
64A ALA* 1.3 61.5 + - - +
66A ALA* 3.4 3.2 + - - -
67A GLN* 2.9 20.0 + - - +
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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
----------------------------------------------------------
61A ASP 4.6 2.1 + - - +
62A PRO 3.4 0.6 - - - -
63A LYS* 1.3 76.2 - - - +
65A TYR* 1.3 64.1 + - - +
67A GLN* 3.2 9.6 + - - +
68A HIS* 3.0 36.0 + - + +
128A ALA* 4.0 16.2 - - + -
131A LYS* 3.9 23.8 - - - +
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.0 14.6 - + - -
61A ASP 5.2 0.2 + - - -
62A PRO 3.3 8.4 + - - +
64A ALA* 1.3 80.1 - - - +
66A ALA* 1.3 58.6 + - - +
68A HIS* 3.2 5.8 + - + +
69A VAL* 2.9 43.2 + - + +
93A THR* 3.2 41.9 - - + +
104A TRP* 5.8 0.2 - - - -
108A LEU* 5.5 3.8 - - + -
128A ALA* 3.7 17.9 + - + +
129A ILE* 4.0 24.9 - - + -
132A MET* 3.7 46.0 - - + -
188A PHE* 2.6 35.8 + - + +
190A PRO* 3.5 8.6 - - + +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.5 9.6 - - + -
50A GLN* 3.9 23.1 - - + -
53A TYR* 3.9 30.3 - - + -
62A PRO 2.9 17.0 + - - +
63A LYS 3.9 3.4 - - - +
65A TYR* 1.3 80.6 - - - +
67A GLN* 1.3 58.1 + - - +
69A VAL* 3.3 4.6 + - - -
70A PHE* 2.9 30.1 + - - +
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.3 28.8 + - - +
50A GLN* 3.8 14.6 + - - +
63A LYS 2.9 14.2 + - - +
64A ALA* 3.2 12.2 + - - +
66A ALA* 1.3 76.8 - - - +
68A HIS* 1.3 63.8 + - + +
70A PHE* 3.3 6.6 + - - +
71A ARG* 2.9 45.7 + - - +
77A SER* 2.8 27.9 + - - -
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Residues in contact with HIS 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* 3.0 30.6 + - - +
65A TYR* 3.2 6.0 + - + +
67A GLN* 1.3 79.9 - - + +
69A VAL* 1.3 57.6 + - - +
71A ARG* 3.3 15.1 + - - +
72A SER* 3.0 23.7 + - - -
108A LEU* 3.6 17.1 - - + +
111A VAL* 4.3 14.3 - - + +
124A GLU* 3.3 46.5 + - + +
125A ILE* 3.4 29.4 - - + +
128A ALA* 3.7 22.3 - - + +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.8 23.6 - - + -
53A TYR* 4.7 0.7 - - + +
65A TYR* 2.9 36.5 + - + +
66A ALA* 3.7 4.7 - - - +
68A HIS* 1.3 73.0 - - - +
70A PHE* 1.3 63.3 + - - +
72A SER* 2.6 26.1 + - - -
73A PHE* 3.8 4.9 - - - -
89A ALA* 3.9 15.0 - - + +
93A THR* 3.8 29.4 - - + -
104A TRP* 4.2 15.3 - - + -
108A LEU* 4.1 16.4 - - + -
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Residues in contact with PHE 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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44A ILE 3.9 0.4 - - - -
45A THR 3.6 5.2 - - - -
46A ARG* 3.3 48.9 - - + -
49A PHE* 3.9 17.4 - - + -
66A ALA 2.9 17.7 + - - +
67A GLN 3.5 4.3 - - - +
69A VAL* 1.3 77.2 - - - +
71A ARG* 1.3 65.2 + - + +
72A SER 3.3 0.7 + - - -
73A PHE* 3.6 15.4 + - - -
74A ASP* 4.3 6.4 - - - +
76A ASN 3.3 24.7 - - - -
77A SER 3.7 13.7 - - - -
78A ASP 3.7 4.9 - - - -
79A GLY 3.7 16.4 - - - -
80A THR* 3.9 9.6 - - - -
81A LEU* 3.5 45.7 - - + +
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Residues in contact with ARG 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 GLN* 2.9 34.7 + - + +
68A HIS* 3.6 13.8 + - - +
69A VAL 3.2 0.2 - - - -
70A PHE* 1.3 74.3 - - + +
72A SER* 1.3 60.8 + - - +
73A PHE 3.0 3.7 + - - -
74A ASP* 3.1 1.1 + - - -
75A ALA* 2.6 51.5 + - - +
76A ASN* 3.8 17.5 - - - +
77A SER* 2.9 43.2 + - - +
107A SER 5.2 0.3 - - - +
111A VAL* 2.9 43.2 + - - +
112A ASP* 4.4 4.2 - - - +
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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
----------------------------------------------------------
68A HIS 3.0 11.9 + - - -
69A VAL 2.6 20.4 + - - -
71A ARG* 1.3 76.7 - - - +
73A PHE* 1.3 69.4 + - - +
74A ASP* 3.5 0.3 + - - -
75A ALA 4.6 0.9 + - - -
104A TRP* 3.0 40.2 + - - -
107A SER* 3.4 32.5 - - - +
108A LEU* 4.1 15.0 - - - -
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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
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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