Contacts of the helix formed by residues 101 - 116 (chain C) in PDB entry 3QS7
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 ILE 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.8 39.3 - - + -
27C LEU 3.6 23.3 - - - +
28C GLN* 3.7 7.2 - - - +
30C TYR* 2.9 27.4 + - + +
32C VAL* 3.6 22.6 - - + +
60C LEU* 3.3 33.4 - - + -
72C LEU* 5.3 1.6 - - + -
100C ASN* 1.3 72.5 - - - +
102C SER* 1.3 59.3 + - - +
104C LEU* 3.4 4.4 + - + +
105C LEU* 2.9 38.2 + - + +
27D LEU* 4.6 1.3 - - + -
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLN* 3.3 47.2 + - - +
100C ASN* 3.0 10.8 + - - +
101C ILE* 1.3 83.8 - - - +
103C ARG* 1.3 58.8 + - - +
105C LEU* 3.6 6.9 + - - +
106C GLN* 3.1 28.9 + - - +
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Residues in contact with ARG 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 5.3 6.4 - - - +
97C VAL* 6.1 1.4 - - - +
99C THR* 3.2 30.9 + - - +
100C ASN* 2.8 17.1 + - + +
102C SER* 1.3 80.2 + - - +
104C LEU* 1.3 59.1 + - - +
106C GLN* 3.3 5.8 + - + +
107C GLU* 2.7 68.0 + - - +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 3.7 33.4 - - + -
33C THR 4.1 5.4 - - - +
34C VAL* 3.8 26.2 - - + -
49C ARG 5.5 0.9 - - - +
52C LEU* 5.6 0.7 - - + -
53C ALA* 4.0 28.3 - - + +
56C TRP* 3.9 30.1 - - + -
57C MET* 5.1 8.7 - - + -
60C LEU* 5.8 1.1 - - + -
99C THR* 4.9 0.6 - - - +
100C ASN 3.1 5.5 + - - -
101C ILE* 3.4 11.6 + - + +
103C ARG* 1.3 76.5 - - - +
105C LEU* 1.3 58.4 + - + +
107C GLU* 3.5 5.8 + - + +
108C THR* 2.9 33.9 + - - +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.8 33.6 - - + +
22C LEU* 3.3 31.6 - - + -
23C SER* 4.3 9.2 - - - +
26C LEU* 3.5 18.6 - - + -
28C GLN* 5.9 0.2 - - - +
57C MET* 3.4 32.8 - - + -
75C VAL* 4.9 2.5 - - + -
101C ILE* 2.9 28.4 + - + +
102C SER* 3.9 6.7 - - - +
104C LEU* 1.3 74.9 - - + +
106C GLN* 1.3 65.4 + - - +
108C THR* 3.5 6.1 + - - +
109C SER* 3.1 21.8 + - - -
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 5.8 0.2 - - - -
102C SER 3.1 19.5 + - - +
103C ARG* 3.6 7.4 - - + +
104C LEU 3.3 0.2 - - - -
105C LEU* 1.3 76.0 - - - +
107C GLU* 1.3 63.9 + - + +
109C SER* 3.3 12.1 + - - -
110C GLU* 3.1 45.5 + - - +
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 3.9 22.5 - - - +
49C ARG* 5.9 0.2 - - - +
103C ARG* 2.7 55.0 + - - +
104C LEU* 3.8 6.0 - - + +
106C GLN* 1.3 73.6 - - + +
108C THR* 1.3 55.2 + - - +
110C GLU* 3.0 19.7 + - - +
111C GLN* 2.8 56.9 + - - +
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Residues in contact with THR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.4 9.6 - - + -
50C LEU* 3.9 15.4 - - + +
53C ALA* 3.3 24.9 - - - +
57C MET* 5.1 4.5 - - + +
75C VAL* 5.4 6.7 - - + -
79C ILE* 4.0 21.8 - - + -
104C LEU* 2.9 24.6 + - - +
105C LEU* 3.6 9.1 - - + -
106C GLN 3.3 0.2 - - - -
107C GLU* 1.3 75.0 - - - +
109C SER* 1.3 63.4 + - - +
111C GLN* 3.3 12.7 + - - +
112C LEU* 3.0 27.9 + - + +
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Residues in contact with SER 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.6 17.7 - - - -
16C ALA* 4.3 10.4 - - - +
19C ILE* 4.0 20.2 - - - +
105C LEU 3.1 14.0 + - - -
106C GLN* 3.4 18.2 - - - -
107C GLU 3.2 0.2 - - - -
108C THR* 1.3 76.0 - - - +
110C GLU* 1.3 61.9 + - - +
112C LEU* 3.1 5.2 + - - +
113C VAL* 3.0 28.3 + - - +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLN* 3.1 37.9 + - - +
107C GLU* 3.0 22.5 + - - +
109C SER* 1.3 75.7 - - - +
111C GLN* 1.3 57.3 - - + +
113C VAL* 3.2 10.1 + - - +
114C ALA* 3.0 28.6 + - - +
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLY* 3.9 20.5 - - - +
49C ARG* 3.0 31.9 - - - +
50C LEU* 3.4 30.8 + - + +
53C ALA* 4.9 0.5 - - - +
107C GLU* 2.8 41.7 + - + +
108C THR* 3.4 19.7 + - - +
110C GLU* 1.3 69.2 - - + +
112C LEU* 1.3 60.0 + - - +
114C ALA* 3.6 5.4 + - - +
115C LEU* 3.0 32.8 + - - +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.7 33.3 - - + +
15C PHE* 3.4 43.5 - - + -
19C ILE* 4.5 4.9 - - + -
50C LEU* 4.1 15.3 - - + -
78C GLU* 4.0 10.5 - - + +
79C ILE* 3.7 32.3 - - + -
81C PHE* 4.2 2.5 - - + -
108C THR* 3.0 21.5 + - + +
109C SER 3.1 6.9 + - - +
111C GLN* 1.3 75.8 - - - +
113C VAL* 1.3 57.7 + - - +
115C LEU* 3.7 2.7 - - - +
116C LYS* 2.8 31.7 + - - +
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.5 19.7 - - + -
16C ALA* 6.3 0.2 - - + -
109C SER* 3.0 20.1 + - - +
110C GLU* 3.2 10.7 + - - +
112C LEU* 1.3 77.5 - - - +
114C ALA* 1.3 63.4 + - + +
116C LYS* 3.4 6.5 + - - +
117C PRO* 3.3 17.2 - - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLU 3.0 15.8 + - - +
111C GLN* 4.1 5.8 - - - +
113C VAL* 1.3 77.9 - - + +
115C LEU* 1.3 57.1 + - - +
117C PRO* 3.3 18.1 - - - +
118C TRP* 4.8 4.3 + - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.9 13.7 - - + -
43C LEU 4.9 6.5 - - - +
46C GLY* 4.8 3.1 - - - -
47C LEU* 3.8 31.0 - - + +
50C LEU* 3.5 29.6 - - + -
81C PHE* 4.8 1.6 - - + -
111C GLN 3.0 17.0 + - - +
112C LEU* 3.8 3.4 - - - +
114C ALA* 1.3 77.4 - - - +
116C LYS* 1.4 57.0 + - - +
117C PRO* 3.4 0.4 - - - -
118C TRP* 3.1 8.4 + - + +
119C ILE* 2.9 42.1 + - + +
124C PHE* 4.4 27.6 - - + -
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Residues in contact with LYS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 5.7 1.6 - - - -
11C ILE* 3.8 23.3 - - + +
15C PHE* 5.5 3.1 - - + -
112C LEU 2.8 18.1 + - - +
113C VAL* 3.5 8.3 - - - +
115C LEU* 1.4 75.6 - - - +
117C PRO* 1.4 65.7 - - + +
118C TRP 3.4 0.9 + - - -
119C ILE* 3.7 13.6 - - - +
120C THR* 5.7 0.3 + - - -
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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
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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