Contacts of the helix formed by residues 101 - 110 (chain Q) in PDB entry 1XFV
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 SER 101 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95Q ASP* 5.6 0.5 - - - -
97Q ASN* 4.8 4.7 + - - -
99Q TYR 3.7 0.6 + - - -
100Q ILE* 1.3 74.8 - - - +
102Q ALA* 1.3 55.2 + - - +
103Q ALA* 3.8 10.9 - - - +
104Q GLU* 2.6 40.8 + - - +
105Q LEU* 2.8 31.2 + - - -
125Q ILE* 3.7 1.3 - - - -
134Q GLY 5.5 0.2 - - - -
135Q GLN* 4.8 12.8 - - - +
806Q CA 4.2 2.1 - - - -
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Residues in contact with ALA 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q SER* 1.3 69.6 - - - +
103Q ALA* 1.3 69.1 + - - +
105Q LEU* 4.0 0.7 - - - -
106Q ARG* 3.2 17.3 + - - +
121Q VAL* 3.3 18.5 - - + +
122Q ASP* 4.0 19.5 - - - +
125Q ILE* 3.2 43.9 - - + +
134Q GLY 5.1 2.3 + - - +
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Residues in contact with ALA 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q SER* 3.8 12.0 - - - +
102Q ALA* 1.3 83.4 - - - +
104Q GLU* 1.3 58.1 + - + +
106Q ARG* 3.3 16.1 + - - +
107Q HIS* 3.0 24.3 + - - +
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Residues in contact with GLU 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Q PHE* 3.5 21.2 - - - +
93Q ASP* 4.1 1.1 - - - -
94Q LYS* 3.2 22.1 + - + +
95Q ASP* 2.5 22.8 + - - +
99Q TYR 2.9 3.1 - - - +
100Q ILE* 3.2 3.6 - - + -
101Q SER* 2.6 46.1 + - - +
103Q ALA* 1.3 74.5 - - - +
105Q LEU* 1.3 69.8 + - - +
106Q ARG 3.1 1.8 - - - -
107Q HIS* 3.8 10.3 - - + +
108Q VAL* 3.0 24.1 + - - +
806Q CA 1.9 27.2 - - - -
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Residues in contact with LEU 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526C GLN* 3.3 30.5 - - + +
92Q PHE* 4.2 19.6 - - + -
100Q ILE* 4.6 6.5 - - + -
101Q SER 2.8 11.5 + - - +
102Q ALA 3.6 8.1 - - - +
103Q ALA 3.3 0.4 - - - -
104Q GLU* 1.3 75.2 - - - +
106Q ARG* 1.3 59.4 + - - +
108Q VAL* 3.9 2.3 - - - +
109Q MET* 2.9 45.0 + - + +
121Q VAL* 3.8 11.7 - - + -
124Q MET* 3.7 31.9 - - + -
125Q ILE* 3.4 38.6 - - + +
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Residues in contact with ARG 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q ALA 3.2 7.5 + - - +
103Q ALA* 3.5 20.2 + - - +
104Q GLU 3.1 0.4 - - - -
105Q LEU* 1.3 76.0 - - - +
107Q HIS* 1.3 65.2 + - - +
108Q VAL 2.8 4.2 + - - -
109Q MET* 2.8 23.7 + - - -
110Q THR* 2.8 28.4 + - + +
116Q LEU* 3.9 24.8 + - + +
118Q ASP* 3.5 34.7 + - - +
121Q VAL* 3.0 30.3 - - + -
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Residues in contact with HIS 107 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623C ASP* 3.1 28.1 + - - -
94Q LYS* 4.2 25.4 - - + -
103Q ALA 3.0 16.9 + - - +
104Q GLU* 3.2 9.8 + - + +
106Q ARG* 1.3 81.8 - - - +
108Q VAL* 1.3 56.8 + - + +
110Q THR* 3.4 17.4 + - - -
111Q ASN* 3.7 18.0 - - - +
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Residues in contact with VAL 108 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501C LEU* 4.0 24.9 - - + -
623C ASP* 6.4 0.4 - - - -
91Q VAL* 4.3 13.0 - - + +
92Q PHE* 3.3 41.1 - - + -
94Q LYS* 3.9 31.0 - - + -
104Q GLU 3.0 12.4 + - - +
106Q ARG 2.8 1.6 + - - -
107Q HIS* 1.3 75.2 - - + +
109Q MET* 1.3 66.1 + - - +
110Q THR 3.0 3.2 + - - -
111Q ASN* 3.3 14.6 + - - +
112Q LEU* 3.5 21.8 + - + +
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Residues in contact with MET 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C TRP* 5.7 0.2 - - + -
525C LYS* 4.3 7.6 - - + +
526C GLN* 5.2 8.3 - - - -
529C VAL* 3.9 40.4 - - + -
92Q PHE* 4.7 10.8 - - + -
105Q LEU* 2.9 37.5 + - + +
106Q ARG 2.8 4.2 + - - +
108Q VAL* 1.3 77.9 - - - +
110Q THR* 1.3 57.5 + - + +
111Q ASN 3.5 0.4 + - - -
112Q LEU* 4.1 7.1 + - + +
114Q GLU* 2.9 67.7 + - + +
116Q LEU* 3.2 32.8 - - + -
124Q MET* 5.3 2.7 - - + -
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Residues in contact with THR 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q ARG* 2.8 35.0 + - + +
107Q HIS* 3.4 17.1 + - - -
109Q MET* 1.3 79.8 - - + +
111Q ASN* 1.3 71.9 + - - +
112Q LEU 3.4 0.7 - - - -
113Q GLY* 3.5 11.6 + - - -
114Q GLU 3.3 16.9 + - - +
115Q LYS* 5.0 15.7 - - - +
116Q LEU 4.6 7.9 - - - +
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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