Contacts of the helix formed by residues 69 - 78 (chain B) in PDB entry 4JDL
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 PRO 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA* 1.3 89.1 - - + +
70B PRO* 1.3 68.4 - - + +
71B GLU* 3.3 3.4 - - + +
72B SER* 2.8 47.3 + - - +
73B VAL* 3.0 12.5 + - - +
157B SER* 5.4 0.7 - - - +
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Residues in contact with PRO 70 (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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68B ALA 3.5 1.7 - - - +
69B PRO* 1.3 85.4 - - + +
71B GLU* 1.3 57.7 + - + +
73B VAL* 3.1 11.1 + - + +
74B TRP* 2.7 40.1 + - - +
132B HIS* 3.9 21.5 - - + +
154B LEU* 4.1 2.6 - - + +
155B HIS 4.4 2.7 - - - +
156B ALA* 4.3 12.6 - - + -
157B SER* 4.0 31.6 - - - +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 6.0 2.7 - - + -
72A SER* 4.9 14.3 + - - +
69B PRO* 3.3 3.1 - - + -
70B PRO* 1.3 84.0 - - + +
72B SER* 1.3 56.0 - - - +
74B TRP* 3.3 19.4 - - + +
75B ALA* 2.8 33.6 + - - +
129B GLU 5.0 3.3 - - - +
130B GLU* 4.7 3.0 - - - +
132B HIS* 3.2 24.0 + - - -
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 4.9 16.7 - - - +
72A SER* 5.6 5.8 + - - +
75A ALA* 4.2 10.9 - - - +
68B ALA* 4.8 2.9 - - - -
69B PRO* 2.8 40.5 + - - +
71B GLU* 1.3 80.5 - - - +
73B VAL* 1.3 56.9 + - - -
75B ALA* 3.5 16.2 - - - +
76B LEU* 4.8 0.9 + - - +
200B THR* 4.2 16.5 - - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 5.6 12.3 - - + +
68B ALA* 4.3 10.5 - - + +
69B PRO 3.0 12.9 + - - +
70B PRO* 3.2 23.1 - - + +
72B SER* 1.3 72.2 - - - +
74B TRP* 1.3 68.5 + - - +
75B ALA 2.9 2.3 + - - -
76B LEU* 3.1 16.1 + - - +
77B VAL* 3.9 7.3 + - + +
154B LEU* 3.7 15.9 - - + -
157B SER 5.8 2.5 - - - +
163B VAL 5.9 4.5 - - - +
164B VAL* 3.7 21.3 - - + -
196B LEU* 4.7 13.0 - - + +
200B THR* 4.3 20.4 - - - +
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Residues in contact with TRP 74 (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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70B PRO 2.7 22.4 + - - +
71B GLU* 3.3 16.8 - - + +
73B VAL* 1.3 74.0 - - - +
75B ALA* 1.3 66.1 + - - +
77B VAL* 2.9 38.3 - - + +
78B ARG* 3.4 20.9 + - + +
127B LEU* 5.1 1.8 - - + -
128B ASP 3.6 23.3 - - - -
129B GLU* 3.2 42.5 + - + -
132B HIS* 3.2 54.3 - + + +
133B VAL 3.7 1.1 - - - -
134B ILE* 3.4 31.2 - - + -
154B LEU* 3.3 15.4 - - + +
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Residues in contact with ALA 75 (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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72A SER* 4.7 15.7 - - - +
75A ALA* 4.4 16.6 - - + -
76A LEU* 5.6 1.3 - - + +
199A SER 5.5 2.3 - - - +
71B GLU 2.8 16.7 + - - +
72B SER* 3.5 20.0 - - - +
73B VAL 2.9 0.8 + - - -
74B TRP* 1.3 78.2 - - - +
76B LEU* 1.3 60.1 + - + +
78B ARG* 3.4 18.0 + - - +
79B ARG* 4.4 4.0 + - - +
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Residues in contact with LEU 76 (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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75A ALA* 6.3 1.8 - - + -
79A ARG* 6.4 2.7 - - + -
72B SER 5.8 0.7 - - - +
73B VAL 3.1 8.8 + - - +
75B ALA* 1.3 77.8 - - + +
77B VAL* 1.3 66.4 + - - +
78B ARG 3.3 0.5 + - - -
79B ARG* 3.3 14.4 + - - +
85B VAL* 3.4 30.9 - - + +
86B TYR* 4.3 2.5 - - + -
196B LEU* 4.2 14.4 - - + -
200B THR* 6.0 2.2 - - - +
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Residues in contact with VAL 77 (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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73B VAL 3.9 2.2 + - - +
74B TRP* 2.9 51.6 - - + +
76B LEU* 1.3 78.4 - - - +
78B ARG* 1.3 62.2 + - - +
79B ARG 3.0 9.7 + - - +
86B TYR* 3.7 23.7 - - + +
134B ILE* 3.7 22.9 - - + +
152B THR* 4.9 0.7 - - + -
154B LEU* 3.8 18.4 - - + -
164B VAL* 4.8 3.1 - - + -
196B LEU* 3.4 37.5 - - + -
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Residues in contact with ARG 78 (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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198A ARG 3.9 7.9 + - - -
199A SER* 3.0 32.4 + - - +
200A THR* 3.4 2.4 - - - +
201A ASN* 3.1 42.1 - - - +
74B TRP* 3.4 34.1 + - + +
75B ALA* 3.4 16.5 + - - +
76B LEU 3.2 0.2 - - - -
77B VAL* 1.3 81.1 - - - +
79B ARG* 1.3 58.9 + - + +
80B PHE* 2.9 17.5 + - - +
124B LEU* 5.7 0.5 - - - +
127B LEU* 4.7 10.5 - - + +
129B GLU* 3.4 28.7 + - - +
134B ILE* 4.8 5.9 - - + +
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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