Contacts of the helix formed by residues 105 - 116 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 4.3 3.4 - - - +
103A ASN 3.8 7.4 - - - +
104A VAL* 1.3 92.5 - - + +
106A LEU* 1.3 61.4 + - - +
107A ASP* 3.3 16.6 - - - +
108A ILE* 3.3 25.4 + - + -
109A PHE* 2.9 27.0 + - - +
99D ARG* 4.1 20.0 - - + +
100D ARG 5.3 6.7 - - - +
101D PRO* 5.7 4.5 - - + -
102D VAL 6.2 0.4 - - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.6 15.7 - - - +
104A VAL 3.7 0.8 + - - -
105A PRO* 1.3 72.5 - - - +
107A ASP* 1.3 55.3 + - - +
109A PHE* 3.9 0.3 - - - -
110A SER* 2.6 42.2 + - - +
126A PHE* 3.5 36.1 - - + -
130A GLU* 3.5 34.1 - - + +
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PRO* 3.3 19.9 - - - +
106A LEU* 1.3 73.4 + - - +
108A ILE* 1.3 71.5 + - - +
110A SER* 3.4 7.3 + - - -
111A GLU* 2.8 32.5 + - + +
97D ARG* 2.8 28.4 + - - +
99D ARG* 2.0 39.9 + - - +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASN* 4.2 17.3 - - + +
84A SER* 4.3 2.0 - - - +
104A VAL* 4.1 13.9 - - + -
105A PRO* 3.3 27.1 + - + +
107A ASP* 1.3 96.2 + - - +
109A PHE* 1.3 63.5 + - - +
111A GLU* 3.3 11.4 + - - +
112A GLU* 3.1 22.1 + - + +
90D TYR* 3.6 54.1 - - + +
97D ARG* 4.3 1.3 - - - +
99D ARG* 4.0 15.7 - - + -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER* 3.6 41.1 - - - -
87A ALA* 3.8 14.6 - - + -
88A ILE* 4.2 12.8 - - + -
98A LEU* 3.8 22.7 - - + -
99A ARG 3.9 2.7 - - - -
100A ARG* 3.6 37.7 - - + -
101A PRO* 3.7 15.7 - - + -
104A VAL* 3.8 6.7 - - + +
105A PRO 2.9 18.0 + - - +
106A LEU 4.1 0.4 - - - +
108A ILE* 1.3 78.4 - - - +
110A SER* 1.3 61.7 + - - +
112A GLU* 3.1 4.3 + - + +
113A ILE* 3.0 41.3 + - + +
126A PHE* 3.6 19.7 - + + -
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 2.6 30.3 + - - +
107A ASP* 3.5 8.7 - - - -
108A ILE 3.3 0.2 - - - -
109A PHE* 1.3 74.2 - - - +
111A GLU* 1.3 60.6 + - - +
113A ILE* 3.2 14.7 + - - +
114A ARG* 3.0 32.1 + - - +
123A MET* 3.9 15.5 - - - +
126A PHE* 3.7 15.6 - - - -
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 4.3 4.3 + - - +
107A ASP* 2.8 26.6 + - + +
108A ILE* 3.5 6.5 - - - +
109A PHE 3.3 0.2 - - - -
110A SER* 1.3 74.8 - - - +
112A GLU* 1.3 65.4 + - - +
114A ARG* 3.4 9.6 + - - +
115A PHE* 2.9 28.8 + - - +
90D TYR* 3.4 11.0 + - - +
94D SER* 5.8 0.5 - - - -
97D ARG* 2.8 31.1 + - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 2.8 49.3 + - - +
81A ASN* 4.4 18.9 + - + +
84A SER* 3.6 29.6 - - - +
88A ILE* 4.6 6.3 - - + -
108A ILE* 3.1 14.8 + - + +
109A PHE* 3.1 9.0 + - + +
111A GLU* 1.3 77.4 - - - +
113A ILE* 1.3 65.1 + - - +
115A PHE* 3.2 2.4 + - - -
116A TYR* 3.0 48.1 + - + -
90D TYR* 4.9 8.7 + - - -
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 4.5 8.5 - - + -
98A LEU* 3.8 16.8 - - + -
109A PHE* 3.0 47.8 + - + +
110A SER* 3.5 7.0 - - - +
112A GLU* 1.3 75.9 - - - +
114A ARG* 1.3 63.1 + - - +
116A TYR 3.5 1.0 + - - -
117A GLU 3.1 16.6 + - - -
118A LEU* 3.3 29.8 + - + +
119A GLY 5.3 1.8 - - - +
123A MET* 3.8 26.9 - - + +
126A PHE* 3.6 37.5 - - + -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A SER* 3.0 20.9 + - - +
111A GLU* 3.5 9.2 - - - +
113A ILE* 1.3 75.7 - - + +
115A PHE* 1.3 66.0 + - - +
117A GLU* 3.1 21.0 + - - +
120A GLU* 4.6 9.9 + - - -
123A MET* 3.9 38.7 - - - +
127A ARG* 4.5 10.5 - - - +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.5 25.4 - - + +
68A TYR* 3.4 37.9 - + - -
78A PHE* 3.6 13.2 - + - -
80A ARG* 3.4 60.6 - - - +
111A GLU 2.9 12.2 + - - +
112A GLU 3.2 3.6 + - - +
114A ARG* 1.3 76.6 - - - +
116A TYR* 1.3 88.5 + + - +
117A GLU* 3.3 7.5 + - - +
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE* 3.7 13.9 - - - +
57A THR* 3.6 5.7 - - - -
58A LEU* 3.0 27.0 + - + +
59A LEU* 4.2 21.1 - - + -
78A PHE* 4.1 15.9 - + - +
80A ARG* 3.7 16.6 - - - +
81A ASN 5.3 0.9 + - - -
84A SER* 6.0 0.7 - - - -
85A PHE* 3.5 36.0 - + + +
88A ILE* 4.0 25.1 - - + -
92A TYR* 4.5 1.0 + - - +
112A GLU* 3.0 45.8 + - + +
113A ILE 4.3 0.7 - - - +
115A PHE* 1.3 98.4 - + - +
117A GLU* 1.3 67.2 + - - +
118A LEU* 3.4 18.5 + - + +
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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