Contacts of the helix formed by residues 56 - 68 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B ALA* 3.0 26.7 + - + +
54B LYS 3.9 0.4 - - - -
55B THR* 1.3 77.2 - - - +
57B TRP* 1.3 91.3 + - + +
58B ILE 3.5 1.1 - - - -
59B PRO* 3.5 3.0 - - - +
60B ARG* 3.1 45.1 + - - +
76B PHE* 3.5 19.1 - - + -
-10C HIS* 2.9 26.1 + - - +
-9C HIS* 3.7 18.8 + - - -
-6C GLU* 5.1 1.2 + - - -
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Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TRP* 5.3 9.2 - + - -
169A LEU* 5.6 2.2 - - + -
52B ALA* 3.4 29.0 + - - +
53B GLU* 3.8 8.4 + - - -
56B ASN* 1.3 97.1 - - - +
58B ILE* 1.3 60.4 + - - +
60B ARG* 4.9 0.7 - - - -
61B LEU* 2.9 26.0 + - - +
101B ARG* 5.7 0.2 - - - +
104B ASN* 6.3 0.2 - - - +
135B LEU* 3.6 36.2 - - + +
136B LEU* 6.5 0.2 - - - -
138B ALA* 3.7 15.5 - - + -
139B TRP* 3.1 83.2 - + + -
142B HIS* 3.5 37.7 + + + -
143B ASP* 5.7 0.2 + - - -
-9C HIS* 5.0 2.9 - + - -
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA 5.2 0.4 + - - -
53B GLU 5.2 1.5 + - - +
57B TRP* 1.3 76.6 - - - +
59B PRO* 1.3 70.2 - - + +
61B LEU* 3.2 26.6 + - + +
62B ARG* 2.9 58.3 + - + +
104B ASN* 3.5 54.5 - - + +
107B THR* 3.8 11.7 - - + -
108B LEU* 4.1 8.5 - - - +
111B LEU* 4.9 0.2 - - + -
139B TRP* 3.9 19.5 - - + -
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Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU 5.0 2.5 - - - +
54B LYS 3.6 23.6 - - - +
55B THR* 3.7 18.2 - - - +
56B ASN 3.5 11.7 - - - +
58B ILE* 1.3 98.4 - - + +
60B ARG* 1.3 56.8 + - + +
62B ARG* 3.7 11.9 - - + +
63B PHE* 3.1 26.5 + - - +
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TRP* 3.8 14.3 - - - +
55B THR 5.4 0.2 - - - +
56B ASN* 3.1 37.8 + - - +
57B TRP* 3.7 2.9 - - - +
59B PRO* 1.3 75.8 - - + +
61B LEU* 1.3 60.7 + - - +
63B PHE* 3.6 6.6 - - + +
64B ILE* 2.9 32.9 + - - +
73B PHE* 3.5 44.5 - - + +
74B PRO* 4.4 9.1 + - + -
75B ALA* 5.9 0.6 - - - +
76B PHE* 3.4 34.7 - - + -
124B HIS* 3.8 11.5 + - - -
125B PRO* 4.8 6.3 - - - +
135B LEU* 3.9 19.5 - - + -
-6C GLU* 3.1 31.9 + - - -
-5C ASN* 5.4 0.6 + - - -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TRP 2.9 13.6 + - - +
58B ILE* 3.4 25.8 - - + +
60B ARG* 1.3 76.9 - - - +
62B ARG* 1.3 61.7 + - - +
64B ILE* 3.3 5.7 + - - +
65B LEU* 3.0 32.2 + - + +
108B LEU* 3.7 28.5 - - + -
111B LEU* 3.9 19.1 - - + -
112B VAL* 3.9 12.8 - - + -
132B VAL* 3.8 37.9 - - + -
135B LEU* 3.4 14.9 - - + +
136B LEU* 4.4 5.4 - - + -
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 2.9 29.2 + - - +
59B PRO* 3.7 11.9 - - + +
61B LEU* 1.3 76.4 - - - +
63B PHE* 1.3 58.9 + - - +
65B LEU* 3.7 4.6 - - - +
66B GLN* 2.8 40.9 + - - +
107B THR* 3.6 32.7 + - - +
111B LEU* 3.9 25.7 - - + +
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PRO 3.1 15.6 + - - +
60B ARG* 3.6 8.7 - - - +
61B LEU 3.2 0.2 - - - -
62B ARG* 1.3 77.9 - - - +
64B ILE* 1.3 58.5 + - - +
66B GLN* 4.7 6.1 - - - -
67B GLU* 2.7 66.9 + - + +
68B GLY 3.7 1.5 + - - -
71B LYS* 3.4 39.3 - - + -
72B PRO 3.5 19.5 - - - -
73B PHE* 3.9 18.2 - + + -
74B PRO* 3.6 27.8 - - + -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ARG 2.9 19.0 + - - +
61B LEU* 3.3 7.2 + - - +
63B PHE* 1.3 74.0 - - - +
65B LEU* 1.3 62.7 + - + +
68B GLY* 2.8 30.4 + - - +
73B PHE* 3.6 25.6 - - + -
120B ARG* 4.1 5.8 + - + +
121B THR 3.6 20.8 - - - +
122B GLY* 4.1 13.9 - - - +
130B VAL* 4.5 5.6 - - + -
131B LYS 4.3 7.0 - - - +
132B VAL* 3.7 43.3 - - + +
135B LEU* 4.1 21.8 - - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 3.0 29.9 + - + +
62B ARG* 4.0 4.3 - - - +
64B ILE* 1.3 81.0 - - + +
66B GLN* 1.3 59.2 + - - +
68B GLY 4.8 0.3 + - - -
111B LEU* 3.3 52.0 - - + +
112B VAL* 4.4 2.0 - - + -
117B ASP* 4.9 5.8 - - + +
120B ARG* 3.2 66.2 + - + +
132B VAL* 4.2 10.3 - - + -
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 2.8 26.1 + - - +
63B PHE* 4.2 4.8 - - - +
65B LEU* 1.3 79.0 - - - +
67B GLU* 1.3 84.8 + - + +
68B GLY 3.6 0.2 - - - -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PHE* 2.7 60.3 + - + +
66B GLN* 1.3 102.6 + - + +
68B GLY* 1.3 63.4 + - - +
70B HIS* 3.2 30.0 + - - +
71B LYS* 3.6 37.8 + - + +
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PHE* 4.5 2.9 - - - +
64B ILE* 2.8 21.9 + - - +
65B LEU 4.6 0.6 + - - -
66B GLN 3.6 1.2 - - - -
67B GLU* 1.3 81.4 - - - +
69B GLU* 1.3 59.6 + - - -
70B HIS* 3.5 2.8 + - - -
71B LYS 3.7 10.2 - - - +
121B THR 3.5 15.5 - - - -
122B GLY* 3.4 12.0 - - - -
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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