Contacts of the helix formed by residues 67 - 79 (chain W) in PDB entry 2Q4G
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 LEU 67 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39W LEU* 4.0 19.5 - - + +
41W GLU* 4.0 10.6 - - - +
44W CYS* 3.2 27.8 - - - -
62W LEU* 3.9 26.0 - - + -
65W ASN* 2.9 31.7 + - + +
66W GLU* 1.3 74.1 - - - +
68W GLY* 1.3 64.4 + - - +
70W VAL* 5.1 0.2 - - - +
71W GLY* 2.8 29.8 + - - -
72W VAL* 3.9 26.2 - - + +
75W VAL* 4.3 5.8 - - + -
91W LEU* 4.4 3.6 - - + -
94W CYS* 3.5 18.8 + - - +
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Residues in contact with GLY 68 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66W GLU 3.3 3.0 - - - -
67W LEU* 1.3 83.5 - - - +
69W ASP* 1.3 63.9 + - - -
70W VAL 3.2 1.6 - - - -
72W VAL* 3.2 19.9 + - - +
94W CYS 3.2 9.4 + - - -
95W CYS* 3.6 23.5 - - - +
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Residues in contact with ASP 69 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68W GLY* 1.3 71.9 - - - -
70W VAL* 1.3 65.2 + - + +
72W VAL* 3.8 2.1 + - - +
73W HIS* 3.3 21.0 + - - +
95W CYS 3.9 1.5 + - - +
96W LEU* 3.3 17.5 - - - +
97W THR* 2.6 56.7 + - - +
99W ALA* 3.9 10.5 - - + +
100W GLY* 3.6 20.0 + - - +
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Residues in contact with VAL 70 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W GLU* 3.5 29.8 - - + +
67W LEU 5.1 0.2 - - - +
68W GLY 3.2 0.8 - - - -
69W ASP* 1.3 78.4 - - + +
71W GLY* 1.3 65.9 + - - +
73W HIS* 3.1 11.8 + - + +
74W CYS* 3.0 18.2 + - + +
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Residues in contact with GLY 71 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W GLU* 3.3 16.6 - - - +
44W CYS* 3.6 19.0 - - - +
67W LEU* 2.8 28.1 + - - -
70W VAL* 1.3 74.5 - - - +
72W VAL* 1.3 62.6 + - - +
74W CYS* 2.9 14.2 + - - +
75W VAL* 2.9 15.4 + - - +
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Residues in contact with VAL 72 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67W LEU* 3.9 23.0 + - + +
68W GLY 3.2 18.4 + - - +
69W ASP 4.1 1.6 - - - +
71W GLY* 1.3 74.4 - - - +
73W HIS* 1.3 53.2 + - - +
75W VAL* 3.2 7.7 + - - +
76W LEU* 2.8 59.3 + - + +
91W LEU* 3.8 29.8 - - + -
94W CYS* 4.6 10.5 - - + -
96W LEU* 4.1 29.4 - - + -
100W GLY 5.9 0.7 - - - +
104W LEU* 5.5 1.6 - - + -
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Residues in contact with HIS 73 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69W ASP 3.3 13.9 + - - +
70W VAL* 3.1 15.8 + - + +
71W GLY 3.1 0.2 - - - -
72W VAL* 1.3 80.0 - - - +
74W CYS* 1.3 62.5 + - - +
76W LEU* 3.3 1.3 + - - +
77W GLN* 3.1 54.8 + - + +
103W VAL* 3.4 49.9 - - + +
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Residues in contact with CYS 74 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41W GLU* 3.9 16.8 - - - +
44W CYS* 3.1 26.5 - - + +
45W LYS* 3.4 29.6 - - - -
48W SER* 2.8 32.3 + - - -
70W VAL 3.0 5.6 + - - +
71W GLY 2.9 9.5 + - - +
73W HIS* 1.3 75.2 - - - +
75W VAL* 1.3 62.2 + - - +
77W GLN* 3.3 22.5 + - - +
78W GLY 3.3 0.2 + - - -
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Residues in contact with VAL 75 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W CYS* 3.6 31.2 - - + +
47W ILE* 4.6 12.8 - - + -
48W SER* 4.8 4.2 - - - +
51W LEU* 4.8 3.7 - - + +
60W LEU* 3.8 18.6 - - + -
62W LEU* 3.7 32.1 - - + -
67W LEU* 4.3 4.5 - - + -
71W GLY 2.9 16.1 + - - +
72W VAL* 3.6 9.0 - - - +
74W CYS* 1.3 73.9 - - - +
76W LEU* 1.3 69.3 + - + +
78W GLY* 3.1 14.0 + - - -
79W LEU* 3.7 8.1 + - + +
89W LEU* 5.4 1.8 - - + -
91W LEU* 5.1 6.5 - - + -
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Residues in contact with LEU 76 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72W VAL* 2.8 46.3 + - + +
73W HIS* 3.8 4.0 - - - +
75W VAL* 1.3 77.0 - - + +
77W GLN* 1.3 64.0 + - + +
79W LEU* 3.1 24.7 + - + +
80W GLN* 4.0 8.0 - - - +
89W LEU* 4.3 19.5 - - + -
91W LEU* 4.5 4.9 - - + -
100W GLY 5.5 0.7 - - - +
103W VAL* 3.7 20.6 - - + -
104W LEU* 3.8 34.5 - - + -
107W THR* 3.6 38.7 - - + +
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Residues in contact with GLN 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48W SER* 4.2 4.3 + - - +
52W ARG* 3.6 16.2 + - - +
73W HIS* 3.1 41.4 + - + +
74W CYS* 3.6 24.2 - - - +
75W VAL 3.2 0.4 - - - -
76W LEU* 1.3 76.3 - - + +
78W GLY* 1.3 63.3 + - - +
80W GLN* 3.1 39.2 + - - +
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Residues in contact with GLY 78 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W SER* 3.5 30.3 + - - -
51W LEU* 3.9 10.3 - - - +
52W ARG* 3.5 28.8 + - - +
74W CYS 3.3 4.2 + - - -
75W VAL 3.1 9.8 + - - -
76W LEU 3.1 1.2 - - - -
77W GLN* 1.3 80.0 - - - +
79W LEU* 1.3 57.1 + - - +
80W GLN 3.1 3.7 + - - -
81W THR* 4.0 4.5 + - - -
84W CYS* 5.5 0.5 - - - -
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Residues in contact with LEU 79 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51W LEU* 4.8 8.1 - - + -
57W LEU* 4.2 12.1 - - + -
60W LEU* 5.1 1.8 - - + -
75W VAL* 3.7 9.4 + - + +
76W LEU* 3.1 23.0 + - + +
78W GLY* 1.3 76.0 - - - +
80W GLN* 1.3 61.0 + - - +
81W THR 3.3 2.9 + - - +
84W CYS* 3.8 32.8 - - - +
86W ILE* 3.5 28.0 - - + -
89W LEU* 4.0 25.1 - - + -
107W THR* 5.5 0.7 - - + -
111W LEU* 3.6 47.3 - - + +
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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
------------------------------------------------------------
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