Contacts of the helix formed by residues 105 - 117 (chain B) in PDB entry 1QDV
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ARG* 3.4 40.2 - - + +
100B ARG* 4.7 1.8 - - - +
103B ASN 3.6 9.6 - - - +
104B VAL* 1.3 89.3 - - + +
106B LEU* 1.3 65.1 + - - +
107B ASP* 3.3 6.2 + - - +
108B ILE* 3.3 20.8 + - + +
109B PHE* 3.0 19.4 + - - +
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Residues in contact with LEU 106 (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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100B ARG* 3.7 18.3 - - - +
104B VAL 3.6 1.2 + - - -
105B PRO* 1.3 72.5 - - - +
107B ASP* 1.3 57.5 + - - +
110B SER* 2.7 51.1 + - - +
123B MET* 5.2 0.2 - - + -
126B PHE* 3.3 32.1 - - + -
130B GLU* 3.0 30.3 - - + +
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Residues in contact with ASP 107 (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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97A ARG* 3.7 17.7 + - - +
99A ARG* 2.7 46.3 + - - -
105B PRO* 3.6 4.3 - - - +
106B LEU* 1.3 76.0 - - - +
108B ILE* 1.3 78.6 + - - +
110B SER* 3.5 5.4 + - - -
111B GLU* 3.2 28.2 + - - +
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Residues in contact with ILE 108 (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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90A TYR* 3.5 44.4 - - + +
97A ARG* 3.9 12.8 - - - +
99A ARG* 4.4 16.4 - - + -
81B ASN* 3.7 28.9 - - + +
84B SER* 3.9 7.6 - - - +
104B VAL* 4.1 5.4 - - + -
105B PRO* 3.3 30.5 + - + +
107B ASP* 1.3 90.2 + - - +
109B PHE* 1.3 64.2 + - - +
111B GLU* 3.1 6.3 + - - +
112B GLU* 3.1 22.6 + - + +
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Residues in contact with PHE 109 (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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84B SER* 3.8 30.5 - - - -
87B ALA* 3.4 35.9 - - + -
88B ILE* 4.4 9.6 - - + -
98B LEU* 3.9 16.2 - - + -
99B ARG 3.6 7.4 - - - -
100B ARG* 3.6 39.0 - - + -
101B PRO* 4.1 7.9 - - + -
104B VAL* 4.0 5.6 - - + -
105B PRO 3.0 16.5 + - - +
106B LEU* 4.1 1.3 - - + +
108B ILE* 1.3 76.5 - - - +
110B SER* 1.3 57.1 + - - +
112B GLU* 3.1 3.7 + - + +
113B ILE* 2.9 56.7 + - + +
126B PHE* 4.0 9.4 - + - -
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Residues in contact with SER 110 (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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106B LEU* 2.7 39.8 + - - +
107B ASP* 3.7 6.3 - - - -
109B PHE* 1.3 75.5 - - - +
111B GLU* 1.3 60.9 + - - +
113B ILE* 3.5 9.7 + - - +
114B ARG* 2.8 50.1 + - - +
123B MET* 3.8 9.3 - - - +
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Residues in contact with GLU 111 (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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90A TYR* 3.9 5.4 + - - -
94A SER* 5.7 0.7 - - - -
97A ARG* 2.4 47.2 + - - -
80B ARG* 4.3 5.6 + - - +
107B ASP 3.2 11.4 + - - +
108B ILE 3.1 7.7 + - - +
110B SER* 1.3 78.4 - - - +
112B GLU* 1.3 68.3 + - - +
114B ARG* 3.4 8.8 + - - +
115B PHE* 3.1 23.4 + - - +
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Residues in contact with GLU 112 (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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90A TYR* 4.9 8.5 + - - -
80B ARG* 2.8 48.0 + - - +
81B ASN* 4.0 21.6 + - + +
84B SER* 3.5 30.7 - - - +
88B ILE* 4.5 4.9 - - + -
108B ILE* 3.1 14.9 + - + +
109B PHE* 3.1 9.0 + - + +
111B GLU* 1.3 77.4 - - - +
113B ILE* 1.3 65.6 - - - +
115B PHE* 3.3 2.3 + - - +
116B TYR* 3.0 47.9 + - + -
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Residues in contact with ILE 113 (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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88B ILE* 4.5 7.6 - - + -
98B LEU* 3.4 37.7 - - + -
109B PHE* 2.9 57.9 + - + +
110B SER* 3.9 4.9 - - - +
112B GLU* 1.3 76.0 - - - +
114B ARG* 1.3 65.0 + - - +
116B TYR 3.5 1.0 + - - -
117B GLU 3.1 15.1 + - - -
118B LEU* 3.3 24.3 + - + +
119B GLY 5.2 2.2 - - - +
123B MET* 3.9 32.8 - - + -
126B PHE* 4.4 5.6 - - + -
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Residues in contact with ARG 114 (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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110B SER* 2.8 34.1 + - - +
111B GLU* 3.6 8.5 - - - +
113B ILE* 1.3 78.1 - - - +
115B PHE* 1.3 64.1 + - - +
117B GLU* 2.9 22.1 + - - +
119B GLY 5.5 0.4 + - - -
120B GLU* 5.2 5.7 + - - -
123B MET* 2.8 61.9 - - - +
127B ARG* 5.2 4.6 - - - +
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Residues in contact with PHE 115 (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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58B LEU* 3.3 29.0 - - + +
68B TYR* 3.3 38.8 - + - -
78B PHE* 3.6 19.3 - + - -
80B ARG* 3.4 55.6 - - - +
111B GLU 3.1 14.0 + - - +
112B GLU 3.7 3.1 - - - +
114B ARG* 1.3 81.1 - - - +
116B TYR* 1.3 70.2 + + - +
117B GLU* 3.3 10.6 + - - +
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Residues in contact with TYR 116 (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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39B ILE* 3.7 21.8 - - - +
57B THR* 3.9 4.7 - - - -
58B LEU* 3.0 27.6 + - + +
59B LEU* 4.2 20.4 - - + -
78B PHE* 3.9 17.6 - + - +
80B ARG* 3.8 16.5 - - - +
81B ASN 5.2 0.9 + - - -
84B SER* 6.1 0.7 - - - -
85B PHE* 3.7 19.8 - + - -
88B ILE* 3.8 29.2 - - + -
92B TYR* 4.7 1.3 + - - +
112B GLU* 3.0 47.9 + - + +
113B ILE 4.3 1.1 - - - +
115B PHE* 1.3 96.6 - + - +
117B GLU* 1.3 68.0 + - - +
118B LEU* 3.3 19.8 + - + +
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Residues in contact with GLU 117 (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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56B GLU 4.1 4.3 - - - +
57B THR* 3.4 16.4 - - - +
58B LEU* 4.0 16.3 - - + +
64B LYS* 3.0 41.7 + - - +
113B ILE 3.1 1.8 + - - -
114B ARG* 2.9 18.3 + - - +
115B PHE 3.4 15.6 - - - +
116B TYR* 1.3 80.4 - - - +
118B LEU* 1.3 65.0 + - - +
119B GLY* 3.2 4.0 + - - +
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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