Contacts of the strand formed by residues 125 - 131 (chain B) in PDB entry 3FNV
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 VAL 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.2 4.7 - - + -
72A ASN* 3.5 34.5 - - + +
81A LYS* 3.6 6.1 - - - +
102A TRP* 3.6 28.3 - - + +
101B CYS* 3.8 24.0 - - + -
114B HIS* 3.7 10.3 - - + -
117B HIS* 3.8 17.0 - - + +
118B ASN* 2.8 42.9 + - - +
123B ASP* 3.7 10.5 - - - +
124B ASN* 1.3 79.1 - - - +
126B GLY* 1.3 59.0 + - - +
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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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81A LYS* 4.1 8.3 - - - -
82A VAL 3.1 20.0 + - - -
102A TRP* 3.5 6.5 - - - -
100B ARG* 2.9 26.2 + - - +
114B HIS* 4.3 4.7 - - - -
125B VAL* 1.3 76.1 - - - +
127B PRO* 1.3 72.2 - - - +
200B FES 3.9 6.1 - - - -
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Residues in contact with PRO 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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83A VAL* 3.4 22.6 - - + +
84A ASN 3.3 21.0 + - - -
97B ALA* 4.1 3.4 - - + -
98B TYR 3.2 17.9 - - - +
100B ARG* 3.3 7.8 + - + +
110B CYS* 3.8 27.1 - - + -
114B HIS* 3.7 22.0 - - + +
126B GLY* 1.3 84.5 - - - +
128B LEU* 1.3 63.5 + - - +
129B ILE* 3.9 16.2 - - + -
200B FES 3.9 4.0 - - - -
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Residues in contact with LEU 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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84A ASN* 3.5 21.1 - - + +
86A ILE* 3.6 26.0 - - + -
98A TYR* 3.7 37.5 - - + -
108A PRO* 4.6 3.1 - - + -
128A LEU* 3.8 23.1 - - + -
96B ALA 3.7 1.0 - - - +
97B ALA* 3.4 1.2 - - - -
98B TYR* 2.7 43.3 + - + +
100B ARG* 3.7 23.1 - - + +
127B PRO* 1.3 72.5 - - - +
129B ILE* 1.3 59.8 + - - +
130B LEU* 3.9 19.4 + - + -
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Residues in contact with ILE 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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83A VAL* 3.6 25.8 - - + -
84A ASN 2.8 11.4 + - - +
85A GLU* 3.3 13.7 - - + +
86A ILE* 2.8 27.5 + - - +
95B LYS* 3.4 36.1 - - + -
96B ALA 3.5 4.0 - - - +
97B ALA* 3.3 31.0 - - + -
127B PRO* 3.9 13.7 - - + -
128B LEU* 1.3 75.1 - - - +
130B LEU* 1.3 64.6 + - - +
131B LYS* 3.7 11.1 + - + -
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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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86A ILE* 3.8 13.5 - - + -
88A ILE* 4.3 11.4 - - + -
128A LEU* 5.0 0.4 - - + -
130A LEU* 3.7 40.2 - - + -
86B ILE* 4.3 3.6 - - + -
91B LEU* 4.0 24.4 - - + +
93B LEU 5.1 1.4 - - - +
94B THR 3.8 0.9 - - - +
95B LYS* 3.5 3.8 - - - -
96B ALA* 2.8 35.1 + - + +
98B TYR* 3.5 34.8 - - + -
128B LEU* 3.9 27.6 - - + -
129B ILE* 1.3 74.0 - - - +
131B LYS* 1.3 62.3 + - - +
132B LYS* 4.1 0.5 + - - +
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Residues in contact with LYS 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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85A GLU* 4.4 20.4 - - + -
86A ILE 2.8 15.8 + - - +
87A ASN* 3.9 20.4 - - - +
88A ILE* 3.0 30.7 + - - +
89A GLU 4.5 0.5 + - - -
94B THR 3.3 9.9 - - - +
95B LYS* 4.7 9.9 - - + -
129B ILE* 4.1 17.7 - - + +
130B LEU* 1.3 77.4 - - - +
132B LYS* 1.3 60.1 + - - +
133B LYS 4.2 0.8 + - - -
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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