Contacts of the strand formed by residues 97 - 105 (chain V) in PDB entry 3TDD
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 ALA 97 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46V ALA 4.0 1.8 - - - -
51V ASP 4.4 0.4 - - - +
52V THR* 4.2 10.3 - - - +
55V VAL* 4.0 22.9 - - + -
87V LEU* 3.9 23.7 - - + +
95V ILE* 2.7 18.8 + - + +
96V GLY* 1.3 72.8 - - - -
98V TYR* 1.3 60.5 + - - +
99V LEU* 4.0 10.1 - - + -
113V ILE 4.0 0.5 - - - +
114V HIS 3.5 2.8 - - - -
115V ALA* 3.0 24.3 + - - +
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Residues in contact with TYR 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V ILE* 4.0 1.6 - - - +
44V ALA 3.9 0.3 - - - +
45V GLY* 3.5 1.2 - - - -
46V ALA* 2.7 56.0 + - + +
47V GLY* 4.1 9.4 - - - -
93V GLY 5.5 0.2 + - - -
96V GLY* 3.9 13.9 - - - -
97V ALA* 1.3 72.7 - - - +
99V LEU* 1.3 61.5 + - - +
113V ILE 3.4 3.6 - - - -
114V HIS* 3.8 27.8 - + + -
115V ALA* 3.4 41.3 - - + +
116V HIS* 4.8 8.9 + + - -
127V LEU* 3.9 17.3 - - + -
128V GLY 6.1 0.2 - - - +
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Residues in contact with LEU 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V HIS* 5.7 0.4 - - + -
43V CYS* 3.9 26.9 - - + -
44V ALA 3.2 5.4 - - - +
45V GLY* 3.8 16.2 - - - -
52V THR* 3.8 24.2 - - + +
55V VAL* 4.1 18.6 - - + -
56V THR* 5.1 2.7 - - - +
83V LEU* 4.0 23.1 - - + -
87V LEU* 5.1 4.9 - - + -
97V ALA* 4.2 9.2 - - + +
98V TYR* 1.3 87.2 - - - +
100V ILE* 1.3 65.0 + - - +
101V VAL* 3.8 1.5 + - + +
112V SER* 3.2 3.8 - - - -
113V ILE* 2.8 47.9 + - + +
127V LEU* 3.7 3.7 - - - +
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Residues in contact with ILE 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V ILE* 3.6 35.2 - - + +
4V VAL* 3.8 7.0 - - - -
5V GLY* 4.1 10.5 - - - -
14V ILE* 4.5 8.7 - - + +
42V TRP 4.0 0.2 - - - +
43V CYS* 3.5 2.8 - - - -
44V ALA* 2.9 36.4 + - + +
99V LEU* 1.3 75.6 - - - +
101V VAL* 1.3 59.0 - - - +
102V ALA 4.0 0.9 + - - -
110V LEU* 3.8 23.1 - - + -
111V PHE 3.3 12.1 - - - +
112V SER* 4.7 4.9 - - - -
125V LEU* 3.7 28.7 - - + +
126V SER* 4.0 4.3 - - - -
127V LEU* 3.7 16.2 - - + +
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Residues in contact with VAL 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ILE* 4.3 9.2 - - + -
41V ILE* 4.1 17.3 - - + -
42V TRP 3.7 6.1 - - - +
43V CYS* 3.8 13.5 - - - -
76V VAL* 4.0 18.6 - - + +
79V ALA* 4.9 6.5 - - + -
80V LEU* 3.7 30.1 - - + +
83V LEU* 4.8 4.3 - - + -
99V LEU* 5.0 1.1 - - + +
100V ILE* 1.3 72.2 - - - +
102V ALA* 1.3 63.6 + - - +
110V LEU* 3.7 1.1 - - - -
111V PHE* 2.9 46.6 + - + +
113V ILE* 4.1 13.2 - - + -
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Residues in contact with ALA 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V VAL* 3.6 25.1 - - + -
14V ILE* 3.8 20.6 - - + -
41V ILE* 3.3 7.8 - - - +
42V TRP 2.9 29.6 + - - +
76V VAL* 4.3 6.3 - - - -
100V ILE 4.0 0.4 + - - -
101V VAL* 1.3 76.0 - - - +
103V GLY* 1.3 59.3 + - - +
109V HIS 3.2 15.5 - - - +
110V LEU* 3.9 4.3 - - + -
178V MET* 3.8 7.0 - - + -
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Residues in contact with GLY 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V VAL* 3.7 4.0 - - - +
40V LYS 3.0 14.8 - - - -
41V ILE* 4.0 0.2 - - - -
76V VAL* 3.7 16.7 - - - +
102V ALA* 1.3 79.8 - - - +
104V VAL* 1.3 64.5 + - - +
108V SER* 3.4 1.9 - - - -
109V HIS* 2.9 28.5 + - - -
178V MET* 3.5 10.3 - - - -
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Residues in contact with VAL 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V VAL* 4.9 0.2 - - + -
40V LYS* 3.0 45.6 + - + +
41V ILE* 4.7 2.6 - - - +
74V PRO 4.7 1.7 - - - +
76V VAL* 4.9 0.4 - - - -
103V GLY* 1.3 80.6 - - - +
105V ASP* 1.3 66.2 + - - +
107V GLY 3.2 6.7 - - - +
108V SER* 3.7 19.5 - - - -
178V MET* 3.6 29.1 - - + +
179V GLU 3.8 14.4 - - - +
180V ILE* 3.8 25.8 - - + +
184V ALA* 6.2 0.2 - - + -
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Residues in contact with ASP 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V PRO* 1.3 67.3 - - + +
73V GLU* 5.4 1.8 - - - -
74V PRO 3.2 20.0 - - - +
75V ARG* 3.2 10.0 - - - +
76V VAL* 2.8 29.7 + - + +
77V VAL* 4.7 0.5 + - - +
104V VAL* 1.3 75.9 - - - +
106V THR* 2.7 39.7 + - - -
107V GLY* 2.8 20.8 + - - +
109V HIS* 3.4 15.9 + - - -
180V ILE* 6.1 1.4 - - - +
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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