Contacts of the helix formed by residues 67 - 79 (chain A) in PDB entry 2R5N
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 GLY 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A HIS 4.3 1.1 - - - -
29A ALA* 4.4 7.2 - - - -
30A PRO* 3.7 26.0 - - - -
62A LEU* 3.4 11.6 - - - +
64A ASN 3.1 10.4 + - - -
65A GLY 3.1 2.0 - - - -
66A HIS* 1.3 79.9 - - - +
68A SER* 1.3 55.6 + - - -
69A MET 3.2 3.1 - - - -
70A LEU* 2.9 31.7 + - - +
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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
----------------------------------------------------------
62A LEU* 4.0 7.4 - - - -
65A GLY 3.1 11.3 + - - -
66A HIS 2.9 4.8 + - - -
67A GLY* 1.3 75.7 - - - +
69A MET* 1.3 62.7 + - - +
71A ILE* 3.1 16.6 + - - +
72A TYR* 3.1 29.9 + - - -
90A PHE* 3.3 17.3 - - - -
99A GLY 2.7 28.1 + - - -
101A PRO* 3.9 14.6 - - - -
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Residues in contact with MET 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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14A LEU 3.6 11.7 - - - +
15A SER* 3.5 25.6 - - - +
18A ALA* 3.4 35.7 - - + -
19A VAL* 4.2 5.2 - - + -
26A HIS 5.3 1.1 + - - +
30A PRO* 4.5 5.6 - - + +
66A HIS 4.9 0.2 + - - -
67A GLY 3.2 1.0 + - - -
68A SER* 1.3 80.3 + - - +
70A LEU* 1.3 54.7 + - - +
72A TYR* 3.9 13.9 - - + -
73A SER* 2.8 47.7 + - - +
87A LEU* 4.0 23.8 - - + +
90A PHE* 3.7 40.8 - - + -
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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
----------------------------------------------------------
11A ILE* 3.6 24.2 - - + -
15A SER* 4.3 1.6 - - - -
29A ALA* 4.8 1.1 - - + +
30A PRO* 3.8 29.1 - - + +
33A MET* 3.9 19.5 - - + -
34A ALA* 4.5 2.7 - - - -
37A ALA* 3.8 21.8 - - + -
60A PHE* 5.7 0.2 - - + -
62A LEU* 3.9 13.7 - - + -
67A GLY 2.9 14.3 + - - +
69A MET* 1.3 78.0 - - - +
71A ILE* 1.3 62.2 + - - +
73A SER* 3.4 2.3 + - - -
74A LEU* 3.1 35.3 + - + +
152A PHE* 3.8 30.1 - - + -
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Residues in contact with ILE 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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41A TRP* 4.8 4.9 - - + -
60A PHE* 4.0 35.0 - - + +
62A LEU* 4.1 17.0 - - + +
67A GLY 4.0 0.6 + - - -
68A SER 3.1 16.2 + - - +
70A LEU* 1.3 76.7 - - - +
72A TYR* 1.3 71.6 + - + +
74A LEU* 3.2 6.6 + - - +
75A LEU* 2.8 49.1 + - + +
101A PRO* 3.8 26.7 - - + -
108A GLY 4.6 4.5 - - - +
109A VAL* 4.2 26.9 - - + -
110A GLU 5.3 1.8 - - - +
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Residues in contact with TYR 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 SER* 3.1 28.4 + - - +
69A MET* 3.9 24.7 - - + +
71A ILE* 1.3 86.9 - - + +
73A SER* 1.3 57.3 + - - +
75A LEU* 4.7 1.3 - - + -
76A HIS* 2.9 31.9 + - - +
82A LEU* 3.7 20.0 - - + +
87A LEU* 4.1 19.1 - - + +
90A PHE* 3.9 4.0 - + - -
96A LYS 4.0 10.8 - - - -
97A THR* 3.6 24.9 - - + -
98A PRO* 2.6 46.2 + - - +
101A PRO* 3.4 13.5 - - + +
102A GLU 4.5 0.2 + - - -
106A THR* 4.1 12.6 - - + -
109A VAL* 4.4 6.5 - - + -
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Residues in contact with SER 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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11A ILE* 3.7 26.3 + - - -
14A LEU* 3.5 29.8 - - - +
15A SER* 3.4 11.8 + - - -
69A MET* 2.8 26.5 + - - +
70A LEU 3.6 4.5 - - - -
72A TYR* 1.3 77.5 - - - +
74A LEU* 1.3 57.2 + - - +
76A HIS* 3.8 0.7 - - - +
77A LEU* 2.8 38.5 + - - +
87A LEU* 4.6 2.9 - - - -
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Residues in contact with LEU 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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11A ILE* 3.8 14.8 - - + -
37A ALA* 3.9 20.6 - - + -
41A TRP* 3.7 52.5 - - + +
60A PHE* 4.8 7.2 - - + -
70A LEU* 3.1 30.5 + - + +
71A ILE* 3.6 9.0 - - - +
73A SER* 1.3 76.3 - - - +
75A LEU* 1.3 60.6 + - - +
77A LEU* 4.8 3.1 - - - -
78A THR* 2.9 33.7 + - - +
294A TRP* 3.7 32.8 - - + -
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Residues in contact with LEU 75 (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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41A TRP* 3.8 20.2 - - + -
71A ILE* 2.8 35.6 + - + +
72A TYR* 4.0 3.8 - - + +
74A LEU* 1.3 71.5 - - - +
76A HIS* 1.3 62.6 + - - +
79A GLY 3.3 3.5 + - - -
80A TYR* 2.9 60.7 + - + +
82A LEU* 4.0 11.0 - - + -
106A THR* 4.3 8.1 - - + -
107A ALA 3.4 23.8 - - - +
108A GLY* 3.9 13.7 - - - +
109A VAL* 3.8 25.4 - - + -
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Residues in contact with HIS 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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14A LEU* 4.4 7.0 - - + -
72A TYR 2.9 18.4 + - - +
73A SER 3.8 2.0 - - - +
75A LEU* 1.3 77.6 - - - +
77A LEU* 1.3 71.6 + - + +
79A GLY* 3.2 13.3 + - - -
80A TYR 4.8 2.6 + - - +
82A LEU* 2.8 31.7 + - + +
83A PRO* 3.8 2.7 - - + -
84A MET* 3.3 41.8 + - + +
87A LEU* 4.2 15.9 - - + -
291A TYR* 2.6 43.1 + + - -
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Residues in contact with LEU 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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10A ALA* 4.1 11.9 - - + -
11A ILE* 4.1 16.6 - - + -
14A LEU* 4.1 21.8 - - + -
73A SER 2.8 28.7 + - - +
74A LEU 4.1 1.1 - - - +
76A HIS* 1.3 77.3 - - + +
78A THR* 1.3 61.4 + - - +
79A GLY 3.4 1.0 + - - -
286A ILE* 4.2 25.6 - - + -
290A ILE* 4.9 0.2 - - + -
291A TYR* 4.2 21.1 - - + -
294A TRP* 3.4 66.1 - - + +
295A ASP* 3.7 5.4 + - - +
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Residues in contact with THR 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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41A TRP* 3.9 22.5 - - + +
42A ARG* 5.8 0.4 - - + -
47A HIS* 3.8 6.0 - - + +
49A PRO* 3.3 11.2 - - - +
74A LEU 2.9 26.4 + - - +
77A LEU* 1.3 74.6 - - - +
79A GLY* 1.3 56.6 + - - +
80A TYR* 3.3 24.9 - - - -
294A TRP* 3.4 37.9 - - + +
295A ASP* 3.6 2.8 - - - +
296A ALA* 2.8 35.6 + - + -
297A LYS 4.0 0.3 + - - -
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Residues in contact with GLY 79 (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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49A PRO* 3.6 15.1 - - - +
50A GLN* 5.4 0.7 - - - +
75A LEU 3.3 0.2 + - - -
76A HIS 3.2 12.6 + - - -
77A LEU 3.3 0.8 - - - -
78A THR* 1.3 78.3 - - - +
80A TYR* 1.3 67.8 + - - +
81A ASP 3.9 0.2 + - - -
295A ASP* 3.5 14.8 - - - -
297A LYS* 4.0 19.8 + - - +
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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