Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 3IVV
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 ASP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ARG* 2.8 26.2 + - - +
87A TYR* 3.8 15.8 - - + +
88A LEU 3.1 18.8 - - - +
89A LEU* 4.0 5.1 - - + +
125A PHE* 4.5 0.2 - - - -
128A GLY 4.1 0.2 + - - -
129A LYS* 1.3 78.5 - - - +
131A TRP* 1.3 70.5 + - - +
100D SER* 2.7 30.5 + - - -
101D THR* 2.7 55.9 + - - +
102D THR* 5.1 0.8 + - - -
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Residues in contact with TRP 131 (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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87A TYR* 3.7 4.5 - - - -
88A LEU* 2.9 32.6 + - - +
102A PHE* 3.8 23.8 - - + -
121A ARG* 5.8 0.9 - - - -
123A TYR* 3.6 36.0 - + + +
124A ARG* 2.8 31.3 + - + -
125A PHE* 3.6 28.7 - + + -
129A LYS* 3.3 27.5 - - + +
130A ASP* 1.3 80.0 - - - +
132A GLY* 1.3 58.9 + - - +
98D VAL* 3.6 13.9 - - + -
99D THR* 3.4 29.4 - - - -
100D SER* 3.6 15.7 - - - -
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Residues in contact with GLY 132 (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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86A LEU 3.3 11.7 - - - -
87A TYR* 3.5 5.5 - - - -
102A PHE* 3.9 16.2 - - - -
104A PHE* 4.7 0.7 - - - -
131A TRP* 1.3 77.0 - - - +
133A PHE* 1.3 65.0 + - - -
134A LYS 4.0 1.1 + - - -
98D VAL* 3.3 9.0 - - - +
99D THR* 2.9 34.1 + - - -
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Residues in contact with PHE 133 (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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85A SER* 3.5 1.6 - - - -
86A LEU 2.9 33.0 + - - +
87A TYR* 4.3 1.8 - - - -
102A PHE* 3.8 18.4 - + - -
104A PHE* 3.9 18.6 - + - -
117A MET* 3.5 61.7 - - + -
118A GLU 3.7 16.6 - - - -
119A SER 4.0 1.1 - - - -
132A GLY* 1.3 72.5 - - - -
134A LYS* 1.3 64.9 + - - +
135A LYS 3.2 1.9 + - - +
136A PHE* 3.6 25.1 + + + +
96D ASP 3.0 28.5 - - - -
97D GLU* 3.6 12.6 - - + +
98D VAL* 3.6 17.9 - - + -
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Residues in contact with LYS 134 (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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76A LEU* 4.0 13.4 - - + +
77A ASP* 2.8 36.6 + - - +
79A GLU* 3.0 28.4 + - - +
80A SER* 3.5 23.7 - - - +
83A TYR* 4.0 1.6 - - - +
84A LEU 3.6 1.4 - - - +
85A SER* 2.7 28.4 + - - +
87A TYR* 3.4 20.8 + - - +
132A GLY 4.0 2.6 + - - -
133A PHE* 1.3 72.9 - - - +
135A LYS* 1.3 63.0 + - + +
97D GLU 4.8 2.4 + - - -
99D THR* 4.1 23.7 + - + +
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Residues in contact with LYS 135 (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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79A GLU* 3.0 56.9 + - - +
80A SER* 4.2 5.6 - - - +
83A TYR* 3.6 46.8 - - + +
117A MET* 3.7 12.1 - - - +
133A PHE* 3.2 2.8 - - - +
134A LYS* 1.3 85.8 - - + +
136A PHE* 1.3 64.7 + - - +
137A ILE 3.5 2.0 - - - -
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Residues in contact with PHE 136 (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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84A LEU* 3.1 21.9 + - + +
86A LEU* 3.9 25.6 - - + -
104A PHE* 3.7 36.1 - - + -
105A SER* 4.2 7.0 - - - -
106A ILE* 4.0 25.4 - - + -
115A LYS* 3.5 33.1 + - + +
117A MET* 3.4 39.2 - - + +
133A PHE* 3.6 26.2 + + + +
134A LYS 3.5 0.4 - - - -
135A LYS* 1.3 76.6 - - - +
137A ILE* 1.3 73.7 + - + +
157A LEU* 4.5 3.1 - - + -
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Residues in contact with ILE 137 (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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83A TYR* 3.3 8.5 - - - -
84A LEU* 2.9 43.8 + - + -
106A ILE* 3.6 25.4 - - + -
115A LYS* 3.7 31.6 - - + +
135A LYS 3.5 0.4 - - - -
136A PHE* 1.3 97.1 - - + +
138A ARG* 1.3 71.8 + - - +
141A PHE* 3.8 7.6 - - + -
142A LEU* 4.3 18.8 - - + -
149A LEU* 3.8 22.4 - - + -
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Residues in contact with ARG 138 (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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82A ASP* 3.5 37.9 + - - +
83A TYR* 3.6 33.9 + - + +
115A LYS* 5.8 0.6 - - - +
137A ILE* 1.3 77.2 - - - +
139A ARG* 1.3 58.9 + - - +
140A ASP* 3.0 37.0 + - - +
141A PHE* 3.7 12.6 - - + +
142A LEU* 3.0 28.5 + - - +
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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