Contacts of the strand formed by residues 105 - 111 (chain H) in PDB entry 3V4V
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 105 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101H TYR* 3.2 9.1 - - - -
102H ASP* 2.7 41.8 + - + +
103H GLY 3.4 0.8 - - - -
104H TRP* 1.3 80.5 + - - +
106H TYR* 1.3 60.3 + - - +
35L ASN* 3.7 17.0 - - - +
36L THR 4.2 7.4 + - - +
37L TYR* 3.8 3.0 - - - -
54L TYR* 4.1 17.7 - - + -
55L GLY* 3.8 18.2 - - - +
58L ASN* 3.4 23.4 + - - -
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Residues in contact with TYR 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H TRP* 3.3 26.2 - + - +
35H HIS* 2.8 38.2 + + - -
50H GLU* 4.2 3.6 + - - -
99H GLY 3.8 0.5 - - - -
100H GLY* 3.5 25.6 - - - -
101H TYR* 3.5 36.8 - + - -
102H ASP 4.9 0.2 - - - +
105H ASP* 1.3 75.8 - - - +
107H ALA* 1.3 88.2 + - - +
108H ILE* 4.2 7.2 - - + -
37L TYR* 3.5 43.5 - + + +
39L SER* 4.7 2.9 + - - -
54L TYR* 4.3 10.5 - - - +
55L GLY 4.6 4.5 + - - -
96L GLY* 6.0 3.8 - - - -
101L TYR* 5.3 8.7 - + - -
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Residues in contact with ALA 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H GLY* 3.3 3.3 - - - -
100H GLY 3.1 29.7 + - - +
106H TYR* 1.3 84.2 - - - +
108H ILE* 1.3 66.1 + - - +
109H ASP* 3.9 4.9 + - + +
39L SER* 4.6 5.8 - - - +
51L LEU* 4.1 11.7 - - + -
54L TYR* 3.5 32.8 - - + -
60L PHE* 6.2 0.2 - - + -
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Residues in contact with ILE 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H HIS* 3.5 42.6 - - + +
47H TRP* 5.3 3.1 - - + +
97H ALA* 3.4 31.0 - - + +
98H ARG 3.3 17.3 - - - +
99H GLY 4.5 0.2 - - - +
106H TYR* 4.2 7.0 - - + -
107H ALA* 1.3 79.1 - - - +
109H ASP* 1.3 59.5 + - - +
111H TRP* 3.6 7.5 + - + +
39L SER* 4.9 0.8 + - - -
41L TYR* 2.5 44.6 + - + +
51L LEU* 4.1 2.5 - - - +
94L LEU* 4.6 17.0 - - + -
101L TYR* 5.1 8.5 - - + -
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Residues in contact with ASP 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H TYR* 5.5 0.9 - - - -
98H ARG* 2.7 54.1 + - - +
99H GLY* 5.8 0.9 - - - -
107H ALA* 5.3 4.4 - - + +
108H ILE* 1.3 72.3 - - - +
110H TYR* 1.3 77.3 + - - +
111H TRP* 3.0 19.9 + - - -
49L PRO 4.8 0.9 - - - +
50L GLN* 5.0 0.3 - - - -
51L LEU* 3.6 27.7 + - + +
60L PHE* 3.5 36.1 - - + -
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Residues in contact with TYR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLN 5.5 2.3 + - - -
2H VAL* 3.7 57.1 + - + +
3H GLN* 5.6 0.7 - - - -
4H LEU* 3.4 11.6 - - + +
97H ALA* 3.4 3.3 - - - +
98H ARG* 2.9 60.8 + - + -
109H ASP* 1.3 87.7 + - - +
111H TRP* 1.3 61.7 + - - +
60L PHE* 3.7 32.2 - + - -
61L SER* 4.2 7.8 + - - -
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Residues in contact with TRP 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H GLN* 5.5 0.5 - - - -
4H LEU* 4.1 16.0 + - - +
37H VAL* 3.7 32.8 - - + -
45H LEU* 4.7 5.8 - - + -
95H TYR* 3.5 41.7 - + + -
96H CYS 3.6 4.3 - - - -
97H ALA* 3.8 16.9 - - + +
108H ILE* 3.6 10.2 + - + -
109H ASP 3.0 24.9 - - - -
110H TYR* 1.3 78.5 - - - +
112H GLY* 1.3 65.5 + - - +
113H GLN* 5.6 0.3 + - - -
41L TYR* 3.4 36.8 - + - -
48L SER* 4.0 12.0 + - - +
49L PRO* 3.7 45.0 + - + +
94L LEU* 5.8 0.7 - - + -
103L PHE* 4.4 15.5 - + - -
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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