Contacts of the helix formed by residues 109 - 118 (chain A) in PDB entry 3VTW
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ASP 4.4 6.3 - - - +
72A HIS* 5.5 3.1 - - - +
73A VAL 3.9 7.2 - - - +
74A ASN* 4.2 4.0 - - + -
107A SER 4.2 3.6 - - - +
108A THR* 1.4 91.9 + - - +
110A ILE* 1.3 60.1 + - - +
111A SER* 4.0 13.5 - - - +
112A GLU* 3.0 49.8 + - + +
113A VAL* 3.2 9.1 + - - +
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Residues in contact with ILE 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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46A ILE* 3.7 19.6 - - + +
48A VAL* 4.2 15.9 - - + -
69A VAL* 3.7 28.5 - - + -
70A PRO 3.4 22.9 - - - +
71A ASP 3.6 6.7 - - - +
73A VAL* 3.0 24.6 + - + +
75A MET* 3.3 31.0 - - + -
78A LEU* 4.0 12.3 - - + -
108A THR 3.7 0.8 + - - -
109A PRO* 1.3 70.4 - - - +
111A SER* 1.3 66.1 + - - +
112A GLU 3.1 0.4 - - - -
113A VAL* 3.8 1.1 - - + +
114A TYR* 3.0 19.1 + - - +
124A LEU* 4.4 8.1 - - + -
126A MET* 4.7 0.2 - - + -
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Residues in contact with SER 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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46A ILE* 4.0 20.0 - - - -
71A ASP* 3.2 24.4 + - - +
109A PRO* 4.0 9.0 - - - +
110A ILE* 1.3 77.5 - - - +
112A GLU* 1.3 62.4 + - - +
114A TYR* 3.4 4.5 + - - +
115A GLU* 3.3 27.1 + - - +
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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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108A THR* 4.1 12.4 - - - +
109A PRO* 3.0 38.4 + - + +
111A SER* 1.3 77.7 + - - +
113A VAL* 1.3 59.1 + - - +
115A GLU* 3.3 6.2 + - - +
116A SER* 2.7 32.9 + - - -
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Residues in contact with VAL 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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75A MET* 3.8 44.2 - - + -
98A VAL* 4.8 9.9 - - + -
103A MET* 5.0 4.9 - - + -
106A VAL* 4.7 6.3 - - + -
108A THR* 3.4 21.8 - - + +
109A PRO 3.2 4.0 + - - +
110A ILE 4.1 1.8 - - - +
111A SER 3.5 0.2 - - - -
112A GLU* 1.3 74.2 - - - +
114A TYR* 1.3 53.4 + - - +
115A GLU 3.3 0.2 + - - -
116A SER* 3.3 4.3 + - - -
117A GLU* 2.8 49.4 + - + +
118A LYS 4.2 0.2 + - - -
124A LEU* 4.2 16.6 - - + +
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Residues in contact with TYR 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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35A VAL* 3.8 13.3 - - - +
39A ARG* 3.7 29.1 + - - -
46A ILE* 3.4 28.5 - - + -
47A PRO* 3.9 23.2 - - + +
110A ILE 3.0 19.7 + - - +
111A SER 3.4 5.8 - - - +
112A GLU 3.2 0.2 - - - -
113A VAL* 1.3 77.3 - - - +
115A GLU* 1.3 74.8 + - + +
118A LYS* 3.0 63.2 + - + +
122A GLY* 2.6 34.0 + - - -
124A LEU* 4.0 16.3 - - + +
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Residues in contact with GLU 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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39A ARG* 4.2 9.0 + - - -
111A SER* 3.3 16.2 + - - +
112A GLU* 3.3 4.9 + - - +
113A VAL 3.2 0.2 - - - -
114A TYR* 1.3 95.8 - - + +
116A SER* 1.3 62.3 + - - +
118A LYS* 3.5 31.6 + - - +
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Residues in contact with SER 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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112A GLU 2.7 19.5 + - - -
113A VAL* 4.0 3.0 + - - -
115A GLU* 1.3 79.5 - - - +
117A GLU* 1.3 83.7 + - - +
118A LYS 3.8 1.2 - - - +
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Residues in contact with GLU 117 (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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98A VAL* 3.5 20.8 - - + +
99A ASN* 3.1 33.0 - - - +
101A HIS* 3.9 25.0 + - - -
113A VAL* 2.8 28.1 + - + +
116A SER* 1.3 103.0 - - - +
118A LYS* 1.3 65.6 + - - +
119A ASP* 3.6 4.7 + - - +
124A LEU* 3.8 11.0 - - + +
125A TYR 5.2 0.7 + - - -
80B LYS* 6.5 0.2 - - - -
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Residues in contact with LYS 118 (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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114A TYR* 3.0 58.9 + - + +
115A GLU* 3.5 35.1 + - - +
116A SER 3.8 0.7 - - - +
117A GLU* 1.3 80.9 - - - +
119A ASP* 1.3 72.1 + - - +
122A GLY* 4.6 5.8 - - - -
123A PHE 3.7 8.7 - - - +
124A LEU* 4.1 6.5 - - - +
80B LYS* 4.6 11.3 + - - +
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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