Contacts of the helix formed by residues 80 - 100 (chain F) in PDB entry 2Q7M
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 GLN 80 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F GLY 3.4 2.0 + - - +
8F ASN* 2.8 29.6 - - + +
9F VAL* 2.4 39.9 - - - +
10F VAL 3.1 0.6 - - - +
11F LEU* 2.8 37.2 - - + +
12F LEU* 3.8 15.6 - - + +
75F GLY* 3.5 20.0 + - - +
79F SER* 1.3 71.4 - - - +
81F VAL* 1.3 59.6 + - + +
84F ALA* 3.1 25.3 + - - +
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Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 5.6 3.4 - - - -
79F SER* 3.9 11.2 - - - -
80F GLN* 1.3 73.7 - - + +
82F PRO* 1.3 87.1 - - + +
83F ALA 3.2 0.7 - - - -
84F ALA* 3.1 5.1 + - - +
85F PHE* 2.8 23.3 + - + +
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Residues in contact with PRO 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F SER* 2.8 32.5 - - - +
81F VAL* 1.3 106.8 - - + +
83F ALA* 1.3 54.0 + - - +
85F PHE* 3.0 6.6 + - + +
86F ALA* 2.7 38.1 + - - +
121F PHE* 4.4 9.1 - - + -
125F MET* 3.7 18.2 - - - -
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Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 4.6 0.7 - - + -
71F LEU* 3.1 25.2 - - - +
74F ALA* 2.8 38.8 - - + +
75F GLY* 3.4 10.1 - - - +
79F SER 3.2 9.0 - - - +
80F GLN 4.5 1.3 - - - -
81F VAL 3.2 0.2 - - - -
82F PRO* 1.3 80.8 - - - +
84F ALA* 1.3 56.4 + - - +
87F GLY 3.1 16.1 + - - -
122F LEU* 3.8 8.7 - - - +
125F MET* 3.0 12.1 - - + +
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Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU* 3.4 31.2 - - + +
12F LEU* 3.6 14.1 - - + +
15F VAL* 3.3 14.8 - - + +
71F LEU* 4.3 3.4 - - - -
80F GLN 3.1 21.4 + - - +
81F VAL* 3.1 4.7 + - - +
83F ALA* 1.3 76.4 - - - +
85F PHE* 1.3 65.0 + - - +
87F GLY 3.6 0.2 + - - -
88F LEU* 3.1 15.6 + - - +
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Residues in contact with PHE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PHE* 4.1 35.2 - + + -
144B GLU 5.0 1.3 - - - -
145B ASN* 5.2 7.0 - - + -
81F VAL* 2.8 14.9 + - + +
82F PRO* 3.6 9.2 - - + +
84F ALA* 1.3 73.9 - - - +
86F ALA* 1.3 65.4 + - - +
87F GLY 3.0 1.1 - - - -
88F LEU* 2.5 46.0 + - + +
89F MET* 3.0 36.1 + - + -
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F PRO 2.7 14.1 + - - +
85F PHE* 1.3 81.3 - - - +
87F GLY* 1.3 60.7 + - - +
88F LEU 3.2 0.2 + - - -
89F MET 3.2 0.3 + - - -
90F TYR 3.1 4.3 + - - -
118F ILE* 2.8 36.3 - - + +
121F PHE* 3.4 22.0 - - + -
122F LEU* 3.4 35.7 - - + -
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Residues in contact with GLY 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.7 7.4 - - - -
67F PHE* 3.9 19.3 - - - -
71F LEU* 4.2 8.7 - - - -
83F ALA 3.1 17.8 + - - -
84F ALA 3.9 2.0 - - - -
85F PHE 3.0 1.0 - - - -
86F ALA* 1.3 76.8 - - - +
88F LEU* 1.3 58.6 + - - +
90F TYR* 3.6 4.4 - - - +
91F LEU* 3.0 27.5 + - - +
122F LEU* 3.8 6.9 - - - +
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.7 12.6 - - + -
18F ILE* 6.1 2.2 - - + -
84F ALA 3.1 11.2 + - - +
85F PHE* 2.5 35.8 + - + +
87F GLY* 1.3 70.9 - - - +
89F MET* 1.3 97.1 + - + +
91F LEU* 3.0 24.1 + - + +
92F PHE* 3.3 39.2 + - + -
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Residues in contact with MET 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 6.2 0.7 - - + -
143B PHE* 4.6 6.7 - - - +
144B GLU 3.4 31.6 - - - +
146B TYR* 4.0 23.6 - - + +
85F PHE* 3.0 27.3 + - + -
86F ALA 3.2 0.9 + - - +
88F LEU* 1.3 95.7 - - + +
90F TYR* 1.3 57.0 + - - +
92F PHE* 2.6 38.5 + - + +
93F VAL* 2.8 21.4 + - + +
118F ILE* 3.5 21.3 - - + -
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Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D 2CS 4.5 2.7 - - - -
63F ALA* 3.0 37.5 + - - +
64F TYR* 5.6 0.7 - + - -
67F PHE* 3.0 53.7 - + + +
86F ALA 3.1 11.9 + - - +
87F GLY 3.6 4.3 - - - +
88F LEU 3.1 0.2 - - - -
89F MET* 1.3 76.8 - - - +
91F LEU* 1.3 60.3 + - + +
92F PHE 3.1 0.2 - - - -
93F VAL* 3.8 7.5 - - + +
94F ARG* 2.9 63.5 + - + +
114F PHE* 3.7 27.8 - + - +
115F GLY* 4.8 4.7 - - - -
118F ILE* 3.2 27.7 - - + +
119F ILE* 3.8 15.0 - - + -
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Residues in contact with LEU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.6 23.1 - - + +
18F ILE* 3.4 34.5 - - + -
19F SER* 3.1 28.5 - - - -
22F GLN* 3.4 29.1 + - - +
67F PHE* 4.6 6.1 - - + -
87F GLY 3.0 23.0 + - - +
88F LEU* 3.0 13.5 + - + +
90F TYR* 1.3 87.6 - - + +
92F PHE* 1.3 66.8 + - + +
94F ARG* 4.0 9.9 - - - +
95F GLN* 3.4 15.8 + - - +
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Residues in contact with PHE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR* 6.2 2.9 - + - -
88F LEU* 3.6 42.8 - - + -
89F MET* 2.6 30.9 + - + +
91F LEU* 1.3 79.2 - - + +
93F VAL* 1.3 64.2 + - + +
94F ARG 3.2 0.7 - - - -
95F GLN* 3.2 8.4 + - + +
96F LYS* 2.9 30.0 + - + +
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F MET* 3.2 23.6 - - + +
90F TYR* 3.8 10.1 - - + +
92F PHE* 1.3 76.5 - - + +
94F ARG* 1.3 54.7 + - - +
96F LYS* 3.1 5.8 + - - +
97F TYR* 2.7 41.0 + - + +
114F PHE* 3.6 19.7 - - + -
115F GLY* 4.0 22.0 - - - +
118F ILE* 4.9 7.4 - - + -
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Residues in contact with ARG 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F SER* 3.8 1.8 + - - -
22F GLN* 2.7 41.0 + - - +
23F ASN* 2.3 45.0 + - - +
26F PHE* 3.7 15.9 - - + -
60F CYS* 3.1 32.0 + - - +
64F TYR* 4.3 15.3 - - - +
90F TYR* 2.9 46.2 + - + +
91F LEU* 3.9 7.1 - - - +
92F PHE 3.2 0.2 - - - -
93F VAL* 1.3 77.5 - - - +
95F GLN* 1.3 55.4 + - - +
97F TYR* 3.9 0.2 - - - +
98F PHE* 2.8 35.5 + - - +
114F PHE* 3.0 36.5 - - + -
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Residues in contact with GLN 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLN* 3.5 9.0 + - - +
25F PHE* 3.9 16.8 - - - -
26F PHE* 2.8 36.7 - - - -
91F LEU 3.4 11.9 + - - +
92F PHE* 3.2 13.4 + - + +
93F VAL 3.1 0.2 - - - -
94F ARG* 1.3 81.3 - - - +
96F LYS* 1.3 78.4 + - + +
98F PHE* 3.7 1.0 - - - -
99F VAL* 2.9 53.8 + - - +
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Residues in contact with LYS 96 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F PHE* 2.9 21.2 + - + +
93F VAL* 3.5 5.2 - - - +
95F GLN* 1.3 103.6 - - + +
97F TYR* 1.3 58.6 + - - +
99F VAL* 3.9 18.6 - - + +
100F GLY* 3.5 15.3 + - - -
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Residues in contact with TYR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 2.8 39.1 - + - -
56F ALA 4.6 1.8 - - - -
59F ASN* 3.1 27.7 + - + +
60F CYS* 4.3 6.1 - - - -
93F VAL* 2.7 23.3 + - + +
94F ARG 3.9 0.2 - - - +
96F LYS* 1.3 71.6 - - - +
98F PHE* 1.3 64.3 + - - +
99F VAL 3.0 5.5 + - - -
100F GLY 3.5 0.5 + - - -
101F TYR* 3.1 27.6 + + + +
110F PRO* 4.3 9.9 - - + -
111F GLY 3.2 20.4 + - - -
112F TYR 4.0 2.4 + - - -
113F ILE 4.0 10.8 - - - -
114F PHE* 3.4 42.0 - + + -
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Residues in contact with PHE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F PHE* 4.5 9.0 - + - -
26F PHE* 3.0 69.1 - + + -
29F LYS* 4.2 19.1 - - + -
53F VAL* 4.2 12.3 - - + -
56F ALA* 3.5 33.5 - - + +
57F ASN* 3.4 28.9 - - + -
60F CYS* 4.1 5.2 - - - -
94F ARG 2.8 20.6 + - - +
95F GLN* 4.1 3.1 - - - +
97F TYR* 1.3 79.6 - - - +
99F VAL* 1.3 61.2 + - + +
101F TYR* 4.2 5.6 + - - -
102F LEU* 4.6 6.5 - - + +
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Residues in contact with VAL 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F PHE* 6.4 1.3 - - + -
95F GLN* 2.9 35.1 + - - +
96F LYS* 3.9 23.6 - - + +
97F TYR 3.0 0.6 - - - -
98F PHE* 1.3 78.5 - - + +
100F GLY* 1.3 69.3 + - - +
101F TYR 3.0 5.0 + - - -
102F LEU* 3.3 22.6 + - - +
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Residues in contact with GLY 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F LYS 3.5 10.5 + - - -
97F TYR* 4.0 1.6 - - - -
99F VAL* 1.3 81.9 - - - +
101F TYR* 1.3 55.1 + - - +
102F LEU 2.9 12.0 + - - -
103F GLY* 3.8 9.8 + - - -
105F ARG* 5.2 4.5 + - - -
110F PRO* 4.5 10.6 - - - +
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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