Contacts of the helix formed by residues 100 - 109 (chain A) in PDB entry 3QV2
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 ALA 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PRO 6.0 0.2 - - - -
83A PRO* 4.2 7.8 - - + +
84A TYR* 3.7 21.8 - - - +
94A ASP 3.7 18.6 - - - +
97A ASP 2.9 12.1 + - - +
99A ARG* 1.3 76.6 - - - +
101A LYS* 1.3 65.9 + - - +
102A SER 3.2 2.7 - - - -
103A VAL* 3.2 11.1 - - + +
104A LEU* 3.1 27.9 + - + +
134A VAL* 4.1 8.7 - - + -
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Residues in contact with LYS 101 (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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60A ASP* 3.4 42.4 + - + +
61A SER* 5.4 2.0 - - - +
97A ASP 3.6 2.8 + - - +
98A PRO* 3.2 25.2 + - + +
100A ALA* 1.3 78.7 - - - +
102A SER* 1.3 57.5 + - - +
104A LEU* 3.9 8.6 - - - +
105A HIS* 3.0 30.6 + - + +
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Residues in contact with SER 102 (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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12A PHE* 3.2 21.7 - - - -
59A LEU* 3.6 31.3 - - - +
60A ASP* 3.1 21.8 + - - -
80A PRO* 4.5 1.4 - - - +
98A PRO 4.7 0.6 + - - -
99A ARG 4.0 13.0 + - - -
101A LYS* 1.3 75.4 - - - +
103A VAL* 1.3 62.6 + - - +
105A HIS* 3.3 3.6 + - - +
106A LEU* 3.2 28.3 + - - +
323A SAH 3.9 9.9 + - - -
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Residues in contact with VAL 103 (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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12A PHE* 4.5 7.0 - - + -
77A MET* 4.2 5.2 - - + -
79A PRO* 3.6 37.0 - - + -
80A PRO* 5.8 0.4 - - + -
84A TYR* 4.0 10.8 - - - +
99A ARG 5.5 0.2 - - - +
100A ALA* 3.2 15.5 - - - +
102A SER* 1.3 78.4 + - - +
104A LEU* 1.3 67.1 + - - +
106A LEU* 3.6 4.2 + - - +
107A TYR* 3.1 42.2 + - + -
123A ILE* 6.0 0.4 - - + -
129A PHE* 5.3 2.2 - - + -
134A VAL* 4.0 22.7 - - + -
138A ILE* 3.8 18.9 - - + +
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Residues in contact with LEU 104 (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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95A ILE* 3.6 44.4 - - + +
97A ASP 5.7 0.2 - - - +
100A ALA* 3.1 23.8 + - + +
101A LYS* 3.9 6.7 - - - +
103A VAL* 1.3 78.8 - - - +
105A HIS* 1.3 57.1 + - - +
107A TYR* 3.3 2.1 + - - +
108A ARG* 2.8 70.0 + - + +
134A VAL* 3.8 31.2 - - + +
137A GLU* 4.1 13.2 - - + +
138A ILE* 4.8 6.1 - - + -
141A ILE* 6.5 0.2 - - + -
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Residues in contact with HIS 105 (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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59A LEU 3.0 21.3 - - - +
60A ASP 3.4 21.4 + - - +
61A SER* 4.3 5.2 - - - -
62A ILE* 2.7 40.6 + - + -
63A SER* 5.7 0.2 - - - -
101A LYS* 3.0 19.6 + - + +
102A SER 3.4 5.2 - - - +
104A LEU* 1.3 78.0 - - - +
106A LEU* 1.3 60.5 + - + +
108A ARG* 4.7 0.7 - - - +
109A ASP* 2.7 76.7 + - + +
110A ILE* 3.5 8.4 + - + +
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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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11A PHE* 3.8 37.9 - - + -
12A PHE* 4.2 15.0 - - + -
59A LEU* 4.5 5.8 - - + +
62A ILE* 4.3 13.9 - - + -
67A ILE* 4.1 18.6 - - + -
75A TRP* 3.6 16.4 - - + -
77A MET* 3.7 25.4 - - + -
102A SER 3.2 16.2 + - - +
103A VAL* 3.8 8.7 - - - +
104A LEU 3.3 0.2 - - - -
105A HIS* 1.3 80.3 - - + +
107A TYR* 1.3 60.6 + - + +
110A ILE* 3.1 11.3 + - + +
111A LEU 3.0 24.9 + - - -
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Residues in contact with TYR 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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75A TRP* 4.3 5.8 - + - -
77A MET* 3.3 35.4 - - + +
103A VAL* 3.1 30.7 - - + +
104A LEU* 3.3 2.9 + - - +
105A HIS 3.3 0.4 - - - -
106A LEU* 1.3 78.4 - - + +
108A ARG* 1.3 61.1 + - - +
111A LEU* 3.8 23.1 - - + +
112A PRO* 3.1 26.3 - - - +
121A ILE* 3.4 14.3 - - + +
123A ILE* 3.1 27.3 - - + +
138A ILE* 3.7 33.7 - - + -
141A ILE* 3.4 26.6 - - + +
142A LEU* 3.7 25.8 - - + -
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Residues in contact with ARG 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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95A ILE* 3.9 20.2 + - - +
104A LEU* 2.8 50.1 + - + +
105A HIS* 5.4 0.4 - - - +
107A TYR* 1.3 76.0 - - - +
109A ASP* 1.3 74.8 + - - +
110A ILE 3.7 0.2 - - - -
112A PRO* 3.6 13.4 - - - +
113A TYR* 3.8 9.0 + - - -
137A GLU* 2.6 42.5 + - - +
141A ILE* 3.9 12.8 - - + -
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Residues in contact with ASP 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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64A ILE* 3.3 24.2 - - + +
105A HIS* 2.7 52.2 + - + +
108A ARG* 1.3 89.5 - - - +
110A ILE* 1.3 62.7 + - + +
113A TYR* 3.4 14.5 - - - -
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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