Contacts of the helix formed by residues 56 - 68 (chain A) in PDB entry 2RD9
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ALA* 3.1 17.1 + - + +
54A LYS 3.9 0.4 - - - -
55A THR* 1.3 77.6 - - - +
57A TRP* 1.3 96.7 + - + +
58A ILE 3.6 1.3 - - - -
59A PRO* 3.4 3.2 - - - +
60A ARG* 3.1 37.1 + - - +
76A PHE* 3.5 21.3 - - + -
-10D HIS* 3.1 32.5 + - - +
-9D HIS* 3.4 22.2 + - - -
-6D GLU* 5.1 0.4 + - - -
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Residues in contact with TRP 57 (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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52A ALA* 3.5 31.2 + - + +
53A GLU* 4.0 8.2 + - - -
56A ASN* 1.3 98.4 - - - +
58A ILE* 1.3 60.1 + - - +
60A ARG* 6.3 0.2 - - - -
61A LEU* 2.9 25.7 + - - +
104A ASN* 6.3 0.4 - - - +
135A LEU* 3.4 45.7 - - + +
138A ALA* 3.7 24.5 - - + -
139A TRP* 3.2 66.4 - + + -
142A HIS* 3.4 36.3 + + + -
143A ASP* 5.6 0.2 + - - -
165B TRP* 5.2 10.1 - + - -
169B LEU* 5.4 3.1 - - + -
-9D HIS* 5.2 2.0 - + - -
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Residues in contact with ILE 58 (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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52A ALA 5.4 0.2 + - - -
53A GLU 5.3 1.3 + - - +
57A TRP* 1.3 73.9 - - - +
59A PRO* 1.3 72.2 - - + +
61A LEU* 3.2 26.7 + - + +
62A ARG* 2.9 52.4 + - + +
104A ASN* 3.6 55.2 - - + +
107A THR* 4.0 15.0 - - + +
108A LEU* 4.2 7.9 - - - +
111A LEU* 5.2 0.2 - - + -
139A TRP* 4.1 17.7 - - + -
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Residues in contact with PRO 59 (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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53A GLU 5.0 3.4 - - - +
54A LYS 3.6 24.9 - - - +
55A THR* 3.8 17.7 - - - +
56A ASN 3.4 13.2 - - - +
57A TRP 3.9 0.4 - - - +
58A ILE* 1.3 98.1 - - + +
60A ARG* 1.3 59.1 + - + +
62A ARG* 3.8 10.4 + - + +
63A PHE* 3.3 22.3 + - - +
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Residues in contact with ARG 60 (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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55A THR 5.4 0.7 - - - +
56A ASN* 3.1 34.1 + - - +
57A TRP* 6.3 0.4 - - - -
59A PRO* 1.3 74.2 - - + +
61A LEU* 1.3 61.6 + - - +
63A PHE* 3.3 6.7 + - - +
64A ILE* 2.9 33.9 + - + +
73A PHE* 3.3 44.5 - - + -
74A PRO* 3.0 25.6 + - + -
75A ALA* 4.0 6.5 - - - +
76A PHE* 3.4 38.3 - - + -
124A HIS* 4.5 3.8 + - - -
125A PRO* 4.7 1.4 - - - +
135A LEU* 3.8 20.6 - - + -
165B TRP* 4.0 9.9 - - - +
-6D GLU* 3.0 27.5 + - - -
-5D ASN* 5.5 0.6 + - - -
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Residues in contact with LEU 61 (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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57A TRP 2.9 18.1 + - - +
58A ILE* 3.2 28.9 + - + +
60A ARG* 1.3 76.9 - - - +
62A ARG* 1.3 62.2 + - - +
64A ILE* 3.2 4.3 + - + +
65A LEU* 3.0 39.6 + - + +
108A LEU* 3.9 24.7 - - + -
111A LEU* 4.0 13.2 - - + -
112A VAL* 3.9 11.7 - - + -
132A VAL* 3.7 36.1 - - + -
135A LEU* 3.4 14.5 - - + +
136A LEU* 4.5 7.6 - - + -
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Residues in contact with ARG 62 (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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58A ILE* 2.9 33.8 + - + +
59A PRO* 3.8 10.3 - - - +
61A LEU* 1.3 73.4 - - - +
63A PHE* 1.3 58.5 + - - +
65A LEU* 3.4 4.2 + - - +
66A GLN* 2.9 33.4 + - - +
107A THR* 3.3 31.6 + - - +
111A LEU* 3.8 29.1 - - + +
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Residues in contact with PHE 63 (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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59A PRO 3.3 12.3 + - - +
60A ARG* 3.3 9.6 + - - +
61A LEU 3.3 0.2 - - - -
62A ARG* 1.3 76.3 - - - +
64A ILE* 1.3 59.5 + - - +
66A GLN* 4.7 1.3 - - - +
67A GLU* 2.7 51.6 + - + +
68A GLY 3.7 1.3 + - - -
71A LYS* 3.5 46.0 - - + -
72A PRO 3.6 13.7 - - - -
73A PHE* 3.5 27.8 - + + -
74A PRO* 3.9 20.6 - - + -
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Residues in contact with ILE 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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60A ARG* 2.9 21.0 + - + +
61A LEU* 3.6 4.7 - - - +
63A PHE* 1.3 79.1 - - - +
65A LEU* 1.3 58.5 + - - +
68A GLY* 2.9 30.5 + - - +
73A PHE* 3.9 31.6 - - + -
120A ARG* 4.2 5.5 + - + +
121A THR 4.0 5.4 - - - +
122A GLY* 3.8 27.6 - - - +
130A VAL* 4.3 11.9 - - + -
131A LYS 5.0 2.9 - - - +
132A VAL* 3.6 29.6 - - + +
135A LEU* 3.9 28.9 - - + -
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Residues in contact with LEU 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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61A LEU* 3.0 33.9 + - + +
62A ARG* 4.0 3.8 - - - +
64A ILE* 1.3 78.4 - - - +
66A GLN* 1.3 59.3 + - - +
68A GLY 4.7 0.9 + - - -
111A LEU* 3.5 50.9 - - + +
112A VAL* 4.5 1.8 - - + -
117A ASP* 4.3 7.0 - - + +
120A ARG* 2.8 58.9 + - + +
132A VAL* 4.1 18.2 - - + -
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Residues in contact with GLN 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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62A ARG 2.9 18.0 + - - +
63A PHE* 4.2 2.2 - - - +
65A LEU* 1.3 79.0 - - - +
67A GLU* 1.3 87.1 + - + +
68A GLY 3.6 0.2 - - - -
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Residues in contact with GLU 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* 2.7 60.9 + - + +
66A GLN* 1.3 105.2 + - + +
68A GLY* 1.3 61.0 + - - +
70A HIS* 2.9 32.9 + - - +
71A LYS* 3.3 37.1 + - + +
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Residues in contact with GLY 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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63A PHE* 3.7 1.9 + - - +
64A ILE* 2.9 21.7 + - - +
65A LEU 4.6 0.8 + - - -
66A GLN 3.6 1.2 - - - -
67A GLU* 1.3 82.5 - - - +
69A GLU* 1.3 57.7 + - - -
70A HIS* 4.6 2.9 - - - -
71A LYS 3.4 17.0 - - - +
121A THR 3.4 14.8 - - - -
122A GLY* 3.6 10.3 - - - -
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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