Contacts of the strand formed by residues 83 - 92 (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 TYR 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LYS 3.7 2.6 - - - -
75A GLY* 3.1 28.1 + - - -
79A GLU 4.9 3.1 - - - -
80A SER* 2.9 13.7 + - - +
81A LYS 3.3 0.4 - - - -
82A ASP* 1.3 95.7 - - + +
84A LEU* 1.3 68.5 + - - +
134A LYS 4.0 3.1 - - - +
135A LYS* 3.6 59.2 - - + +
137A ILE* 3.3 22.7 - - - +
138A ARG* 3.6 34.6 + - + +
139A ARG* 3.6 8.1 - - - +
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Residues in contact with LEU 84 (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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41A PHE* 3.5 31.2 - - + -
71A VAL* 3.4 34.3 - - + -
72A ASN 3.5 8.1 - - - +
73A PRO* 4.3 7.6 - - + +
83A TYR* 1.3 73.1 - - - +
85A SER* 1.3 64.3 + - - +
86A LEU* 4.1 6.5 - - + -
134A LYS 3.6 0.9 - - - +
136A PHE* 3.1 52.8 + - + +
137A ILE* 2.9 20.3 + - + -
139A ARG* 3.8 4.8 - - + +
142A LEU* 4.0 9.6 - - + -
155A LEU* 3.8 16.8 - - + -
157A LEU* 5.2 3.8 - - + -
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Residues in contact with SER 85 (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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71A VAL* 3.3 8.5 - - - +
72A ASN* 2.9 48.9 + - - +
75A GLY* 3.5 4.0 - - - -
76A LEU* 2.9 26.3 + - - +
80A SER* 3.7 1.0 + - - -
84A LEU* 1.3 71.9 - - - +
86A LEU* 1.3 61.5 + - - +
87A TYR* 3.8 14.1 - - - -
133A PHE 3.5 1.3 - - - -
134A LYS* 2.7 26.0 + - - -
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Residues in contact with LEU 86 (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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69A LEU* 4.8 6.3 - - + -
70A ARG 3.7 9.4 - - - +
71A VAL* 4.1 8.7 - - + -
84A LEU* 4.1 7.9 - - + -
85A SER* 1.3 74.7 - - - +
87A TYR* 1.3 68.9 + - - +
104A PHE* 3.3 54.0 - - + -
105A SER 5.6 0.2 - - - +
132A GLY* 3.3 2.4 - - - -
133A PHE* 2.9 35.9 + - - +
136A PHE* 3.9 30.7 - - + -
157A LEU* 3.9 34.1 - - + -
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Residues in contact with TYR 87 (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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69A LEU* 3.3 8.0 - - - +
70A ARG* 2.9 47.2 + - + +
72A ASN* 3.9 11.0 - - - -
76A LEU* 3.3 22.8 - - + +
85A SER* 3.8 19.5 - - - -
86A LEU* 1.3 76.9 - - - +
88A LEU* 1.3 59.1 + - - +
89A LEU 4.0 0.2 - - - -
104A PHE* 3.7 7.3 - - - -
130A ASP* 3.8 27.6 - - + +
131A TRP 3.5 6.1 - - - +
132A GLY* 3.5 26.2 - - - -
133A PHE 4.5 0.2 - - - -
134A LYS* 3.4 25.6 - - - +
99D THR* 3.7 21.7 + - - -
101D THR* 3.5 25.3 + - + -
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Residues in contact with LEU 88 (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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57A PHE* 3.9 15.0 - - + -
67A TRP* 3.7 30.3 - - + -
68A CYS 3.8 8.5 - - - +
69A LEU* 3.8 19.3 - - + -
87A TYR* 1.3 73.4 - - - +
89A LEU* 1.3 57.6 + - - +
102A PHE* 4.0 15.9 - - + -
104A PHE* 3.7 15.5 - - + -
125A PHE* 3.4 26.3 - - + -
130A ASP* 3.1 4.5 - - - -
131A TRP 2.9 34.7 + - - +
159A CYS* 4.3 4.0 - - - -
161A VAL* 3.8 25.8 - - + -
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Residues in contact with LEU 89 (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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53A LYS* 4.4 7.0 - - - +
67A TRP* 3.2 10.5 - - - -
68A CYS* 2.8 61.9 + - - +
70A ARG* 3.6 41.5 - - + +
87A TYR 4.0 1.0 - - - +
88A LEU* 1.3 73.2 - - - +
90A LEU* 1.3 66.1 + - - +
91A VAL* 3.5 11.2 + - + +
128A GLY* 3.4 31.6 - - - +
129A LYS 3.5 14.8 - - - +
130A ASP* 4.0 4.9 - - + +
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Residues in contact with LEU 90 (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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65A LEU* 4.6 2.7 - - + -
66A LYS 3.5 16.8 - - - +
67A TRP* 3.8 34.2 - - + -
89A LEU* 1.3 70.6 - - - +
91A VAL* 1.3 55.3 + - - +
92A SER 3.5 15.5 - - - +
93A CYS* 3.8 26.5 - - + -
98A VAL* 3.8 10.5 - - + -
125A PHE* 3.3 45.8 - - + +
126A VAL 3.8 8.3 - - - +
127A GLN* 4.0 0.4 - - - +
128A GLY* 2.7 36.6 + - - -
129A LYS 3.1 10.6 + - - +
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Residues in contact with VAL 91 (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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53A LYS* 6.0 0.9 - - - +
56A THR* 4.6 11.0 - - + +
66A LYS* 2.7 20.5 + - + +
67A TRP 3.9 23.6 - - - +
68A CYS* 4.0 20.4 - - + +
89A LEU* 4.0 12.6 - - + -
90A LEU* 1.3 73.2 - - - +
92A SER* 1.3 66.8 + - - +
127A GLN* 3.3 15.6 + - - +
128A GLY* 4.0 4.2 + - - +
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Residues in contact with SER 92 (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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64A LYS 3.6 2.6 + - - +
65A LEU* 3.6 0.3 - - - -
66A LYS* 3.0 45.9 + - - +
90A LEU* 3.5 8.9 - - - +
91A VAL* 1.3 86.4 - - - +
93A CYS* 1.3 64.8 + - - +
127A GLN* 3.5 21.5 - - - -
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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