Contacts of the helix formed by residues 66 - 83 (chain A) in PDB entry 4ROE
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 SER 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLN 3.6 4.1 + - - -
65A VAL* 1.3 83.7 - - - +
67A ARG* 1.3 60.8 + - - +
68A SER* 4.3 2.5 - - - -
69A GLN* 3.9 13.1 + - - -
70A GLN* 3.2 23.4 + - - +
101A TYR* 3.7 31.0 + - - -
26N A 4.2 15.3 + - - -
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Residues in contact with ARG 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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66A SER* 1.3 68.4 - - - +
68A SER* 1.4 61.9 + - - +
69A GLN 3.1 1.3 - - - -
70A GLN* 3.1 12.9 + - + +
71A ARG* 3.0 60.5 + - - +
74A ARG* 5.0 2.0 + - - +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 4.3 2.3 - - - -
67A ARG* 1.4 76.1 - - - +
69A GLN* 1.4 55.6 + - - +
71A ARG* 3.9 16.8 + - - +
72A GLY* 3.2 20.8 + - - -
97A TYR* 4.1 6.1 + - - -
101A TYR* 2.7 30.6 + - - -
114A LYS* 4.2 13.7 - - - -
25N C 3.8 23.8 + - - -
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.0 25.2 - - + +
66A SER* 3.7 17.0 + - - +
67A ARG 3.1 0.2 - - - -
68A SER* 1.4 78.4 + - - +
70A GLN* 1.4 58.5 + - - +
72A GLY* 3.1 2.6 + - - -
73A LEU* 2.9 46.7 + - + +
97A TYR* 4.5 2.7 - - + -
98A GLN* 4.1 27.9 + - - +
101A TYR* 3.3 58.1 - - + +
102A ARG* 5.9 2.2 - - - +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.8 24.4 + - + +
66A SER 3.2 16.2 + - - +
67A ARG* 3.1 16.1 + - + +
69A GLN* 1.4 73.7 - - - +
71A ARG* 1.4 56.2 + - - +
73A LEU* 3.5 8.6 + - + +
74A ARG* 3.1 48.0 + - - +
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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
----------------------------------------------------------
67A ARG* 3.0 52.1 + - - +
68A SER* 3.9 13.1 - - - +
70A GLN* 1.4 73.8 - - - +
72A GLY* 1.3 55.9 + - - +
74A ARG* 3.5 33.6 + - - +
75A ARG* 3.1 61.8 + - + +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER 3.2 8.4 + - - -
69A GLN 3.1 7.6 + - - -
71A ARG* 1.3 73.7 - - - +
73A LEU* 1.4 57.0 + - - +
75A ARG* 3.3 7.1 + - - +
76A VAL* 3.0 31.8 + - - +
97A TYR* 3.5 30.7 - - - -
118A VAL* 3.6 8.1 - - - +
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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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65A VAL* 5.6 5.6 - - + -
69A GLN* 2.9 47.8 + - + +
70A GLN* 3.8 8.5 - - + +
72A GLY* 1.4 71.3 - - - +
74A ARG* 1.3 63.3 + - - +
76A VAL* 3.5 10.0 + - - +
77A ARG* 3.3 39.4 + - - +
94A VAL* 4.1 21.9 - - + +
97A TYR* 3.4 23.1 - - + -
98A GLN* 3.6 33.9 - - + +
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Residues in contact with ARG 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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67A ARG* 5.0 2.2 + - - +
70A GLN* 3.1 29.6 + - + +
71A ARG* 3.6 51.3 + - - +
73A LEU* 1.3 75.0 - - + +
75A ARG* 1.4 57.7 + - - +
77A ARG* 3.4 12.1 + - - +
78A ASP* 3.1 38.4 + - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.1 47.3 + - + +
72A GLY* 3.4 7.4 - - - +
74A ARG* 1.4 74.7 - - + +
76A VAL* 1.4 55.9 + - - +
78A ASP* 3.5 9.0 + - - +
79A LEU* 3.0 29.8 + - - +
115A GLU* 3.4 40.5 + - - +
118A VAL* 3.7 23.4 - - + +
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Residues in contact with VAL 76 (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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72A GLY 3.0 18.6 + - - +
73A LEU* 3.5 9.9 - - - +
74A ARG 3.3 0.4 - - - -
75A ARG* 1.4 74.8 - - - +
77A ARG* 1.3 62.8 + - - +
79A LEU* 3.3 4.3 + - - +
80A CYS* 3.1 28.4 + - - -
90A GLU 4.4 1.3 - - - +
93A ALA* 3.7 31.4 - - + +
94A VAL* 3.8 21.5 - - + +
97A TYR* 3.9 28.7 - - + -
118A VAL* 3.8 25.1 - - + +
121A CYS* 4.9 0.9 - - + -
122A VAL* 4.0 5.2 - - + +
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Residues in contact with ARG 77 (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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73A LEU* 3.3 26.5 + - - +
74A ARG* 3.4 11.8 + - - +
76A VAL* 1.3 75.5 - - - +
78A ASP* 1.3 59.3 + - - +
80A CYS* 3.4 1.9 + - - +
81A ARG* 2.9 45.6 + - - +
90A GLU* 3.4 40.9 + - + +
91A ASP* 4.4 14.3 + - - +
94A VAL* 3.6 37.3 - - + +
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Residues in contact with ASP 78 (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 ARG* 3.1 26.9 + - - +
75A ARG* 3.8 8.9 - - - +
76A VAL 3.4 0.2 - - - -
77A ARG* 1.3 73.3 - - - +
79A LEU* 1.3 60.9 + - - +
81A ARG* 3.4 20.0 + - - +
82A VAL* 3.0 37.6 + - + +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG 3.0 17.5 + - - +
76A VAL 3.7 4.7 - - - +
78A ASP* 1.3 76.6 - - - +
80A CYS* 1.4 55.8 + - - +
82A VAL* 3.4 9.6 + - + +
83A LEU* 3.0 52.5 + - + +
118A VAL* 4.1 6.7 - - + -
119A GLY* 3.8 21.8 - - - -
122A VAL* 3.9 13.7 - - + -
138A ILE* 3.6 24.7 - - + -
141A LEU* 4.6 11.4 - - + -
142A LEU* 3.8 27.6 - - + -
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Residues in contact with CYS 80 (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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76A VAL 3.1 18.8 + - - -
77A ARG 3.5 8.3 - - - +
78A ASP 3.4 0.2 - - - -
79A LEU* 1.4 75.3 - - - +
81A ARG* 1.4 56.1 + - - +
83A LEU 3.5 1.2 + - - -
84A GLN 3.2 6.4 + - - -
85A LEU* 3.2 55.1 + - + +
89A PHE 4.5 0.7 - - - -
90A GLU* 3.8 39.7 - - + +
93A ALA* 4.3 8.7 - - - -
122A VAL* 3.8 19.1 - - - -
125A THR* 6.4 0.2 - - - -
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Residues in contact with ARG 81 (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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77A ARG* 2.9 36.1 + - - +
78A ASP* 3.6 21.9 + - - +
79A LEU 3.3 0.2 - - - -
80A CYS* 1.4 72.7 - - - +
82A VAL* 1.3 64.9 + - + +
84A GLN* 3.2 21.0 + - - +
90A GLU* 3.1 30.9 + - - +
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Residues in contact with VAL 82 (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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78A ASP* 3.0 22.4 + - + +
79A LEU* 3.7 12.1 - - + +
81A ARG* 1.3 75.7 - - + +
83A LEU* 1.3 61.3 + - - +
84A GLN* 3.3 8.8 + - - +
141A LEU* 4.3 26.7 - - + -
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Residues in contact with LEU 83 (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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79A LEU* 3.0 24.7 + - + +
80A CYS 3.8 5.4 - - - +
81A ARG 3.3 0.2 - - - -
82A VAL* 1.3 74.5 - - - +
84A GLN* 1.4 68.5 + - - +
85A LEU* 3.4 18.3 + - + +
122A VAL* 3.8 20.2 - - + -
131A TRP* 4.3 11.1 + - - +
133A LEU* 3.6 26.0 - - + -
138A ILE* 3.8 26.2 - - + -
141A LEU* 3.5 28.7 - - + -
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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