Contacts of the helix formed by residues 66 - 76 (chain D) in PDB entry 1R1P
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B PHE* 4.0 22.0 + - - +
58B PRO 5.5 0.3 + - - -
61B PHE 5.2 0.2 + - - -
64D GLY 3.6 2.0 + - - -
65D LEU* 1.3 77.4 - - - +
67D ARG* 1.3 57.9 + - - +
68D HIS* 3.5 6.6 + - - +
69D GLN* 3.0 45.0 + - - +
70D ALA* 2.9 28.2 + - - +
85D ARG* 4.2 1.8 - - - -
88D GLN* 3.2 23.8 - - - -
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D SER* 1.3 71.8 - - - +
68D HIS* 1.3 83.5 + - + +
70D ALA* 3.2 5.7 + - - +
71D GLU* 3.1 23.7 + - - +
85D ARG* 3.5 24.7 - - - +
88D GLN* 4.6 1.4 + - - +
106D HIS* 3.3 37.9 + - + +
556G ASP* 3.2 44.2 + - - +
557G ASP* 3.0 30.7 + - - +
558G PTR 2.8 51.1 + - - +
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Residues in contact with HIS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE 3.8 12.8 - - - +
58B PRO* 4.7 0.9 - - + +
59B GLU* 3.3 58.3 - - + +
66D SER* 3.3 6.0 + - - +
67D ARG* 1.3 94.9 - - + +
69D GLN* 1.3 64.8 + - + +
71D GLU* 3.2 28.2 + - - +
72D ASN* 3.0 30.1 + - - +
556G ASP* 3.9 21.3 + - - -
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B PHE* 2.6 39.1 - - - -
61B PHE 3.1 13.4 + - - +
62B HIS* 3.5 39.3 - - + +
63B GLU* 4.7 4.2 + - - +
64D GLY 3.8 6.1 - - - +
65D LEU* 3.6 23.6 - - + +
66D SER* 3.0 36.5 + - - +
68D HIS* 1.3 76.1 - - + +
70D ALA* 1.3 64.7 + - - +
72D ASN* 3.3 1.6 + - - +
73D LEU* 3.1 27.4 + - - +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LEU* 3.8 22.1 - - + +
66D SER 2.9 13.9 + - - +
67D ARG 3.2 7.2 + - - +
69D GLN* 1.3 75.4 - - - +
71D GLU* 1.3 63.0 + - - +
73D LEU* 3.5 0.9 + - - +
74D LEU* 3.1 28.5 + - - +
83D ILE* 4.1 11.2 - - + -
85D ARG* 3.9 6.5 - - - +
97D SER* 3.5 30.1 - - - +
104D VAL* 4.8 0.4 - - - -
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 5.8 0.2 - - - +
67D ARG* 3.1 15.9 + - - +
68D HIS* 3.2 37.9 + - - +
69D GLN 3.2 0.6 - - - -
70D ALA* 1.3 77.0 - - - +
72D ASN* 1.4 59.1 + - - +
74D LEU 3.2 0.3 + - - -
75D MET* 2.9 39.6 + - + +
104D VAL* 3.7 28.4 - - + +
106D HIS* 2.8 37.5 + - + +
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Residues in contact with ASN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU 3.7 21.0 + - - +
62B HIS* 3.0 40.0 + - + +
65B LEU* 4.6 9.8 - - + +
73B LEU* 3.3 41.8 - - + +
77B LYS* 5.3 4.3 + - - -
83B ILE* 5.0 4.4 - - - +
68D HIS* 3.0 20.1 + - - +
69D GLN* 3.3 3.5 + - - +
71D GLU* 1.4 78.8 - - - +
73D LEU* 1.3 61.4 + - - +
75D MET* 3.7 10.6 + - - +
76D GLY 4.0 4.3 + - - -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 4.0 9.9 - - + +
64B GLY 6.1 0.7 - - - +
65B LEU* 4.0 23.8 - - + -
69B GLN* 4.4 14.6 - - - +
62D HIS* 4.6 11.2 - - + +
65D LEU* 4.2 23.6 - - + -
69D GLN 3.1 13.5 + - - +
70D ALA 3.8 4.5 - - - +
71D GLU 3.1 0.4 - - - -
72D ASN* 1.3 82.3 - - - +
74D LEU* 1.3 60.9 + - - +
76D GLY* 3.6 9.0 + - - -
77D LYS* 3.8 15.8 - - - +
83D ILE* 4.3 19.3 - - + -
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ALA 3.1 20.5 + - - +
71D GLU 3.2 0.2 + - - -
73D LEU* 1.3 74.1 - - - +
75D MET* 1.3 60.8 + - - +
76D GLY 3.1 2.0 - - - -
77D LYS* 2.9 25.1 + - + +
81D PHE* 3.6 39.0 - - + +
82D PHE* 3.7 7.6 - - - +
83D ILE* 3.9 21.1 - - + -
97D SER* 3.3 44.9 - - - +
98D VAL 4.1 2.5 - - - +
99D ARG* 3.1 20.8 + - + +
104D VAL* 3.5 16.6 - - + -
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Residues in contact with MET 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 3.7 31.4 - - + -
77B LYS* 5.6 6.3 - - - +
71D GLU* 2.9 26.0 + - + +
72D ASN 3.9 0.7 - - - +
73D LEU 3.3 0.4 - - - -
74D LEU* 1.3 78.4 - - - +
76D GLY* 1.3 56.3 + - - +
77D LYS 3.3 1.4 + - - +
99D ARG* 3.0 49.9 + - - +
102D ASP 3.9 14.1 - - - +
103D ASP* 3.8 21.3 - - - -
104D VAL* 3.9 9.0 - - + -
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASN* 6.4 1.6 - - - -
73B LEU* 5.7 0.4 - - - +
72D ASN 4.0 4.6 + - - -
73D LEU 3.6 8.2 + - - -
74D LEU 3.1 1.4 - - - -
75D MET* 1.3 75.9 - - - +
77D LYS* 1.3 70.1 + - - +
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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