Contacts of the helix formed by residues 125 - 131 (chain B) in PDB entry 2FV7
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B MET* 4.0 13.0 - - + -
107B GLY* 3.2 3.9 - - - -
123B ILE* 3.9 6.6 + - + +
124B VAL* 1.3 71.8 - - - +
126B GLY* 1.3 65.5 + - - +
128B ASN* 2.9 30.1 + - + +
129B LEU* 3.4 38.6 - - + -
154B GLU 4.8 4.5 - - - +
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Residues in contact with GLY 126 (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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104B ALA* 3.8 12.6 - - - +
105B ALA* 3.4 12.6 - - - -
106B THR 4.9 0.2 - - - -
107B GLY* 4.3 1.6 - - - -
124B VAL* 3.2 16.2 - - - +
125B ALA* 1.3 76.4 - - - +
127B ALA* 1.3 61.0 + - - -
129B LEU* 3.1 22.3 + - - +
130B LEU* 4.1 2.6 + - - +
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Residues in contact with ALA 127 (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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74B LYS* 3.4 19.6 - - - +
75B VAL* 3.5 38.8 - - - +
76B GLY 3.8 0.9 - - - +
101B THR* 3.6 15.3 - - + -
104B ALA* 3.6 11.3 - - - +
105B ALA 2.7 19.9 + - - +
106B THR* 4.4 1.6 - - - -
107B GLY 4.2 0.6 - - - +
125B ALA 3.4 0.8 + - - -
126B GLY* 1.3 67.9 - - - -
128B ASN* 1.3 64.1 + - - +
129B LEU 3.1 0.4 - - - -
130B LEU* 3.0 14.0 + - - +
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Residues in contact with ASN 128 (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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22B GLY 4.4 2.3 - - - +
23B SER* 3.3 11.3 - - - -
24B CYS 3.0 44.7 + - - +
25B MET* 3.7 20.4 - - - +
74B LYS* 3.7 16.6 + - - +
107B GLY* 3.7 4.8 - - - +
125B ALA* 2.9 21.8 + - + +
126B GLY 3.1 0.2 - - - -
127B ALA* 1.3 77.2 - - - +
129B LEU* 1.3 61.4 + - - +
130B LEU 3.2 1.1 + - - -
131B LEU* 3.5 10.8 + - - +
154B GLU 3.6 16.2 - - - +
155B ILE* 3.6 24.8 - - + +
156B THR 4.3 0.3 + - - -
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Residues in contact with LEU 129 (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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125B ALA* 3.4 31.4 - - + -
126B GLY 3.1 13.5 + - - +
128B ASN* 1.3 79.2 - - - +
130B LEU* 1.3 69.5 + - + +
131B LEU 3.4 3.1 - - - +
154B GLU 4.4 2.5 - - - +
155B ILE* 4.1 22.9 - - - +
156B THR* 3.1 24.2 + - - +
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Residues in contact with LEU 130 (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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74B LYS* 2.9 32.7 + - + +
101B THR* 4.2 7.6 - - + +
103B ASP* 3.8 31.0 - - + +
104B ALA* 3.9 22.7 - - + -
126B GLY 4.6 2.7 - - - +
127B ALA 3.0 11.4 + - - +
129B LEU* 1.3 87.3 - - + +
131B LEU* 1.3 63.8 + - - +
132B ASN* 3.1 11.5 + - - +
135B ASP* 3.4 0.2 - - - +
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Residues in contact with LEU 131 (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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21B VAL* 4.1 19.7 - - + -
22B GLY 4.5 3.8 - - - +
72B VAL* 3.8 27.1 - - + +
73B CYS* 3.9 18.2 - - - +
74B LYS* 3.9 11.9 - - + +
99B TYR* 3.9 18.6 - - + -
127B ALA 3.6 3.8 + - - -
128B ASN 3.5 14.3 + - - +
129B LEU 3.4 8.0 - - - +
130B LEU* 1.3 75.2 - - - +
132B ASN* 1.3 52.3 + - - +
135B ASP* 3.5 28.7 - - + +
136B LEU* 5.4 0.9 - - + -
155B ILE* 4.2 15.0 - - + -
156B THR* 4.7 3.5 + - - -
159B THR* 2.8 30.8 + - + -
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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