Contacts of the strand formed by residues 59 - 66 (chain A) in PDB entry 1IVV
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 ARG 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.2 10.0 - - - +
45A LEU* 2.8 53.2 + - + +
57A ASP* 2.9 36.8 + - - +
58A ARG* 1.3 75.9 - - - +
60A PHE* 1.3 60.0 + - - +
76A THR* 4.2 11.2 - - + +
77A VAL 3.1 7.0 - - - +
78A SER* 4.2 0.4 - - - -
85A ILE* 3.0 43.5 - - + +
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Residues in contact with PHE 60 (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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15A ALA* 3.6 31.2 - - + -
19A GLU* 3.3 36.3 - - + -
20A ILE* 3.9 14.8 - - + -
23A VAL* 4.0 20.9 - - + -
42A LEU* 3.9 15.0 - - + -
43A GLY 3.4 6.5 - - - +
44A VAL* 3.5 25.1 - - + -
45A LEU* 4.1 3.4 - - - -
58A ARG* 3.9 10.3 - - + -
59A ARG* 1.3 81.2 - - - +
61A ARG* 1.3 62.5 + - - +
62A VAL* 4.4 3.5 - - + +
75A VAL 3.8 0.3 - - - +
76A THR* 3.2 7.8 - - - +
77A VAL* 2.9 32.8 + - + +
79A VAL* 3.6 22.4 - - + -
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Residues in contact with ARG 61 (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 TYR* 3.9 15.2 - - + +
42A LEU* 3.3 4.2 - - - +
43A GLY 2.7 32.8 + - - +
45A LEU* 3.2 25.5 - - + +
60A PHE* 1.3 71.0 - - - +
62A VAL* 1.3 66.6 + - - +
63A PHE* 3.6 26.3 - - + -
74A GLU* 2.8 37.6 + - + +
75A VAL 3.5 7.0 - - - +
76A THR* 4.6 8.3 - - - +
551A ARG* 3.9 31.5 - - - +
552A TYR* 4.3 10.5 + - - -
556A ASP* 2.9 44.2 + - - -
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Residues in contact with VAL 62 (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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23A VAL* 4.0 26.9 - - + -
27A LEU* 4.2 8.3 - - + -
39A ILE* 3.6 25.1 - - + -
41A TYR 3.2 13.0 - - - +
42A LEU* 4.1 8.7 - - + -
60A PHE 4.4 5.2 - - - +
61A ARG* 1.3 81.2 - - - +
63A PHE* 1.3 73.2 + - - +
64A ILE* 3.9 22.6 + - + -
73A GLN 3.8 0.2 - - - +
74A GLU* 3.5 0.9 - - - +
75A VAL* 2.8 41.9 + - + +
77A VAL* 4.6 5.2 - - + -
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Residues in contact with PHE 63 (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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39A ILE* 3.6 3.6 - - - -
40A ALA* 2.7 34.2 + - + +
41A TYR* 2.9 40.6 + + + +
61A ARG* 3.6 31.2 - - + -
62A VAL* 1.3 78.4 - - - +
64A ILE* 1.3 57.4 + - - +
73A GLN 3.5 4.0 - - - -
74A GLU* 3.3 31.9 - - + -
98A LEU* 3.8 15.7 - - + -
99A PRO* 3.9 14.6 - - + -
252A ARG* 4.3 8.1 - - - -
556A ASP* 3.8 18.2 - - + -
557A PHE* 3.3 35.7 - + - -
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Residues in contact with ILE 64 (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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27A LEU* 3.9 26.5 - - + -
32A LEU* 3.4 22.0 - - + +
33A LEU* 4.6 2.9 - - + -
37A LYS* 3.8 28.9 - - + +
38A ARG 3.4 7.6 - - - +
39A ILE* 4.9 3.6 - - + -
62A VAL* 3.9 15.0 - - + -
63A PHE* 1.3 73.5 - - - +
65A HIS* 1.3 72.0 + - - +
72A PRO* 3.1 8.8 - - - +
73A GLN* 2.8 47.6 + - + +
75A VAL* 3.9 23.3 - - + -
98A LEU* 3.7 2.2 - - - +
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Residues in contact with HIS 65 (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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36A GLU 3.7 0.3 - - - +
37A LYS* 3.3 5.8 - - - -
38A ARG* 2.6 49.2 + - + +
40A ALA* 4.4 8.5 - - + -
63A PHE 3.9 0.2 + - - -
64A ILE* 1.3 77.4 - - - +
66A ASP* 1.3 93.7 + - - +
67A VAL* 3.9 12.4 + - + +
69A GLY* 5.9 0.4 - - - -
70A ALA 5.6 0.4 + - - -
72A PRO* 4.1 8.1 - - - +
98A LEU* 3.8 15.5 - - + +
101A LEU* 3.5 26.7 - - + -
104A GLU* 3.7 11.6 + - - -
151A ARG* 3.6 35.0 + - - +
182A VAL* 4.3 9.6 - - + +
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Residues in contact with ASP 66 (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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36A GLU* 3.4 12.8 - - - +
37A LYS* 3.0 30.4 + - - +
64A ILE 4.2 0.2 + - - -
65A HIS* 1.3 93.1 + - - +
67A VAL* 1.3 58.7 + - - +
68A SER* 2.7 40.6 + - - -
69A GLY* 3.0 18.7 + - - -
70A ALA* 2.9 45.6 + - - +
71A ARG 4.5 2.5 - - - +
72A PRO* 4.7 1.6 - - + +
182A VAL* 5.2 0.3 - - - +
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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