Contacts of the helix formed by residues 66 - 78 (chain B) in PDB entry 1EFP
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 LYS 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B VAL* 1.3 73.4 - - - +
67B GLN* 1.3 70.8 + - - +
68B ALA 2.8 7.1 + - - -
69B ALA* 3.1 19.4 + - - +
85B LEU* 3.7 9.6 - - + +
87B VAL* 4.1 24.4 - - + +
89B ALA 4.9 0.4 + - - -
205B GLU* 3.0 44.0 + - - +
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Residues in contact with GLN 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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9B ARG* 3.7 35.4 + - - +
65B VAL* 3.2 22.9 + - + +
66B LYS* 1.3 82.7 + - - +
68B ALA* 1.3 60.4 + - - +
69B ALA* 3.0 4.4 + - - -
70B GLU* 3.2 22.7 + - - +
92B VAL* 5.0 5.2 - - + +
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Residues in contact with ALA 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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9B ARG* 3.8 20.7 - - + +
62B SER* 3.6 17.2 + - - +
63B ILE 5.2 0.2 - - - -
64B GLY* 5.1 3.8 - - - +
65B VAL* 2.9 24.5 + - + +
66B LYS 2.8 1.0 + - - -
67B GLN* 1.3 77.5 - - - +
69B ALA* 1.3 56.1 + - - +
70B GLU 3.1 0.2 - - - -
71B THR* 2.8 27.1 + - - -
72B LEU* 3.1 7.6 + - - +
85B LEU* 3.3 19.3 - - + -
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Residues in contact with ALA 69 (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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66B LYS 3.1 13.8 + - - +
67B GLN* 3.0 1.1 - - - -
68B ALA* 1.3 77.6 - - - +
70B GLU* 1.3 56.5 - - - +
72B LEU* 3.0 15.5 + - - +
73B ARG* 2.8 36.7 + - + +
85B LEU* 4.1 11.2 - - + +
203B LEU* 4.1 16.1 - - + +
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Residues in contact with GLU 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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9B ARG* 4.8 10.3 + - - +
67B GLN* 3.2 14.7 + - - +
68B ALA 3.1 0.2 - - - -
69B ALA* 1.3 78.5 - - - +
71B THR* 1.3 60.7 + - - +
73B ARG* 3.6 9.7 + - - +
74B THR* 2.9 31.1 + - - +
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Residues in contact with THR 71 (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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7B VAL* 4.0 12.8 - - + +
8B LYS 3.9 22.0 - - - +
9B ARG* 3.3 30.7 - - - +
34B SER* 4.7 4.3 + - - -
35B MET* 3.5 33.0 + - + +
62B SER* 5.1 2.2 - - - -
68B ALA* 2.8 13.2 + - - -
70B GLU* 1.3 77.6 - - - +
72B LEU* 1.3 64.1 + - - +
74B THR* 3.2 9.1 + - - -
75B ALA 3.1 16.5 + - - -
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Residues in contact with LEU 72 (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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7B VAL* 4.3 4.3 - - + -
60B ALA* 3.3 38.8 - - + +
61B VAL 4.0 0.9 - - - -
62B SER* 3.9 22.2 - - - +
68B ALA 3.1 5.7 + - - +
69B ALA* 3.0 10.8 + - - +
71B THR* 1.3 72.6 - - - +
73B ARG* 1.3 58.9 + - - +
75B ALA* 2.8 21.8 + - - +
76B LEU* 2.8 18.4 + - - +
83B ALA* 3.6 16.8 - - + +
84B ILE 3.5 21.1 - - - +
85B LEU* 3.5 32.8 - - + -
203B LEU* 4.1 12.3 - - + -
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Residues in contact with ARG 73 (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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69B ALA* 2.8 28.8 + - + +
70B GLU* 3.8 8.1 - - - +
72B LEU* 1.3 71.4 - - - +
74B THR* 1.3 51.5 + - - +
76B LEU* 3.2 24.4 + - - +
77B ALA* 2.7 35.6 + - - +
195B ILE* 6.3 0.9 - - - -
198B ALA* 2.7 32.1 + - + +
199B LYS* 3.8 44.4 + - - +
201B LYS 2.6 30.5 + - - +
202B PRO 4.3 1.2 + - - -
203B LEU* 3.7 26.0 - - + +
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Residues in contact with THR 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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35B MET* 4.6 15.9 - - + -
40B GLU* 5.5 4.5 - - - +
70B GLU* 2.9 23.5 + - - +
71B THR* 3.3 12.2 - - - -
72B LEU 3.1 0.4 - - - -
73B ARG* 1.3 75.8 - - - +
75B ALA* 1.3 62.1 + - - +
77B ALA* 3.2 8.5 + - - +
78B MET* 3.1 30.5 + - - +
190B ALA* 4.5 9.6 - - + +
195B ILE* 6.4 0.7 - - - -
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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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7B VAL* 4.9 2.5 - - + -
35B MET* 4.0 16.4 - - + -
43B VAL* 4.5 13.8 - - + +
60B ALA* 3.9 24.2 - - + -
71B THR 3.1 10.6 + - - +
72B LEU* 2.8 13.4 + - - +
74B THR* 1.3 74.0 - - - +
76B LEU* 1.3 66.1 + - - +
78B MET* 2.9 19.1 + - - +
79B GLY 3.1 9.2 + - - -
80B ALA* 3.2 9.4 + - + +
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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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72B LEU 2.8 17.0 + - - +
73B ARG* 3.2 50.5 - - - +
75B ALA* 1.3 72.0 - - - +
77B ALA* 1.3 62.7 + - - +
79B GLY 3.2 6.8 + - - -
80B ALA* 3.5 18.5 - - + +
81B ASP 3.9 2.7 - - - +
82B ARG* 3.4 42.2 - - - +
83B ALA* 3.8 9.6 - - + +
198B ALA* 3.8 8.6 - - + +
201B LYS* 3.1 39.0 + - + +
202B PRO 3.8 7.9 - - - +
203B LEU* 4.8 1.6 - - + -
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Residues in contact with ALA 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 ARG 2.7 14.1 + - - +
74B THR* 3.3 13.7 - - - +
75B ALA 3.1 0.2 - - - -
76B LEU* 1.3 78.5 - - - +
78B MET* 1.3 59.5 + - - +
79B GLY* 3.5 0.5 + - - -
190B ALA* 3.4 24.7 - - + +
194B ASN* 3.6 25.7 + - - +
195B ILE* 3.9 17.9 - - + -
198B ALA* 3.5 16.3 - - + +
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Residues in contact with MET 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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35B MET* 5.1 3.6 - - - +
40B GLU* 3.7 40.2 - - - +
43B VAL* 3.9 22.2 - - + -
44B GLU* 3.9 22.0 - - + +
47B ILE* 3.3 14.7 - - + +
74B THR* 3.1 18.9 + - + +
75B ALA* 2.9 11.9 + - - +
77B ALA* 1.3 77.7 - - - +
79B GLY* 1.3 56.5 + - - +
187B PRO* 4.5 2.9 - - + -
188B ARG* 3.6 52.2 + - + +
190B ALA* 4.5 13.7 - - + +
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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