Contacts of the helix formed by residues 62 - 75 (chain A) in PDB entry 3RLG
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 ASN 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLU 3.6 7.3 - - - +
44A TYR* 3.5 21.5 - - - -
60A TYR* 4.6 1.7 - - - -
61A GLU* 1.3 75.4 + - - +
63A PHE* 1.3 67.3 + - - +
64A ASN* 4.5 2.0 - - + +
65A ASP* 3.0 41.6 + - - +
66A PHE 3.1 9.0 + - - -
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Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.6 28.7 - - + -
42A PRO* 3.4 30.1 - - + +
43A GLU 2.9 26.6 + - - +
44A TYR 4.3 2.5 - - - +
45A THR* 3.8 21.8 - - + -
61A GLU 3.4 3.9 + - - -
62A ASN* 1.3 71.8 - - - +
64A ASN* 1.3 63.5 + - - +
66A PHE* 3.1 5.7 + + + +
67A LEU* 2.9 58.5 + - + +
90A PHE* 3.9 19.1 - + - -
109A LEU* 4.1 16.8 - - + -
112A ASN* 3.5 20.4 - - + -
113A LEU* 4.8 5.4 - - + -
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Residues in contact with ASN 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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41A ASN* 6.2 0.2 - - - +
62A ASN* 3.2 3.1 - - + +
63A PHE* 1.3 81.3 - - - +
65A ASP* 1.3 62.7 - - - +
67A LEU* 3.2 8.5 + - - +
68A LYS* 3.1 32.5 + - - +
112A ASN* 3.2 43.1 + - - +
116A HIS* 3.2 37.7 + - + +
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Residues in contact with ASP 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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17A ILE* 3.5 18.7 - - + +
61A GLU* 4.4 12.5 - - + +
62A ASN* 3.0 38.7 + - + +
64A ASN* 1.3 74.5 - - - +
66A PHE* 1.3 66.4 + - - +
68A LYS* 3.1 30.3 + - - +
69A GLY 3.0 18.4 + - - -
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Residues in contact with PHE 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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14A VAL 3.2 27.6 - - - -
15A ASN 3.8 17.5 - - - -
16A ALA 3.7 18.6 - - - -
17A ILE* 4.2 11.2 - - - -
20A ILE* 4.0 14.8 - - + -
31A ILE* 3.9 15.9 - - + -
33A THR* 3.4 25.1 - - + -
45A THR* 3.6 17.7 - - + -
61A GLU* 4.1 11.3 - - + +
62A ASN 3.1 8.9 + - - +
63A PHE* 3.5 8.3 - + - +
65A ASP* 1.3 76.9 - - - +
67A LEU* 1.3 58.9 + - + +
69A GLY* 3.1 2.8 + - - -
70A LEU* 2.8 44.0 + - + -
90A PHE* 4.6 9.2 - + - -
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Residues in contact with LEU 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 PHE* 2.9 46.3 + - + +
64A ASN* 3.5 15.5 - - - +
65A ASP 3.1 0.4 - - - -
66A PHE* 1.3 77.1 - - + +
68A LYS* 1.3 53.0 + - - +
70A LEU* 3.5 8.7 - - + +
71A ARG* 2.7 35.5 + - - +
90A PHE* 3.6 22.7 - - + -
112A ASN 3.5 29.4 - - - +
113A LEU* 3.6 28.7 - - + +
116A HIS* 3.8 15.3 - - + +
117A TYR* 3.8 7.1 - - + +
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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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64A ASN* 3.1 26.0 + - - +
65A ASP* 3.1 29.4 + - - +
67A LEU* 1.3 77.4 - - - +
69A GLY* 1.3 60.1 + - - +
71A ARG* 3.4 5.6 + - - +
72A SER* 3.0 26.1 + - - -
116A HIS* 3.9 38.3 + - + +
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Residues in contact with GLY 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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17A ILE* 4.1 25.1 - - - +
20A ILE* 4.1 6.1 - - - +
65A ASP 3.0 13.1 + - - -
66A PHE 3.1 3.3 + - - -
68A LYS* 1.3 77.9 - - - +
70A LEU* 1.3 60.2 + - - +
72A SER* 3.3 8.4 + - - -
73A ALA* 3.1 21.8 + - - +
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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
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20A ILE* 4.0 10.8 - - + +
31A ILE* 4.0 13.2 - - + -
66A PHE* 2.8 26.5 + - + +
67A LEU* 3.5 7.6 - - + +
69A GLY* 1.3 74.3 - - - +
71A ARG* 1.3 58.1 + - - +
73A ALA* 3.2 3.3 + - + +
74A THR* 2.7 36.0 + - + +
85A LEU* 4.0 21.3 - - + -
88A VAL* 3.7 36.1 - - + -
90A PHE* 3.9 25.8 - - + -
117A TYR* 3.5 22.7 - - + -
129A ILE* 4.8 0.7 - - + -
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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 LEU 2.7 21.7 + - - +
68A LYS* 3.5 7.4 - - - +
70A LEU* 1.3 72.0 - - - +
72A SER* 1.3 62.3 + - - +
74A THR* 2.9 10.8 + - - -
75A THR* 2.7 31.8 + - - +
116A HIS 3.7 17.2 + - - +
117A TYR* 3.3 32.6 - - + +
119A ASN* 2.9 47.3 + - - +
122A ASN* 3.4 3.0 + - - +
123A ASN* 3.0 33.3 + - - +
124A GLY* 4.1 0.6 - - - -
125A GLY 3.7 2.5 - - - +
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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 3.0 14.1 + - - -
69A GLY* 3.5 11.0 - - - -
70A LEU 3.2 0.2 - - - -
71A ARG* 1.3 77.2 - - - +
73A ALA* 1.4 62.4 + - - +
74A THR 3.1 1.4 + - - -
75A THR* 3.6 2.1 + - - -
78A ASN* 3.3 52.4 + - - +
80A LYS* 4.4 10.5 - - - -
81A TYR* 3.6 6.4 - - - -
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Residues in contact with ALA 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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20A ILE* 3.8 29.2 - - + -
21A ASP* 5.5 1.6 - - - +
69A GLY 3.1 12.8 + - - +
70A LEU* 3.2 10.0 + - - +
72A SER* 1.4 75.7 - - - +
74A THR* 1.3 59.3 + - - +
75A THR 3.7 0.4 - - - -
80A LYS* 3.5 16.1 - - + +
82A GLN* 2.8 38.4 + - + +
85A LEU* 4.1 9.0 - - + -
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Residues in contact with THR 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 LEU* 2.7 22.8 + - + +
71A ARG 2.9 1.7 + - - -
73A ALA* 1.3 84.3 - - - +
75A THR* 1.3 60.7 + - - +
76A PRO* 3.7 1.0 - - - +
81A TYR* 3.8 9.0 - - - -
82A GLN 4.9 0.4 - - - -
85A LEU* 3.7 41.3 - - + +
117A TYR* 2.7 31.0 + - - +
125A GLY* 3.4 3.5 - - - -
126A ARG* 2.8 38.5 + - - +
127A ALA* 4.1 9.4 - - + -
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Residues in contact with THR 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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71A ARG* 2.7 39.8 + - - +
72A SER* 3.6 4.4 + - - -
74A THR* 1.3 76.8 - - - +
76A PRO* 1.3 75.7 - - + +
78A ASN* 3.0 28.2 + - + +
81A TYR* 3.3 9.1 - - - -
123A ASN* 3.4 44.4 - - - +
124A GLY 3.7 2.6 - - - +
125A GLY 3.6 7.6 + - - -
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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