Contacts of the strand formed by residues 79 - 85 (chain Y) in PDB entry 1T6B
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 79 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43Y PHE 3.4 6.7 + - - +
44Y ASP* 2.5 43.1 + - - +
45Y LEU* 2.7 29.3 + - - +
76Y PRO 5.6 0.9 - - - +
77Y GLU 4.3 7.2 + - - +
78Y MET* 1.3 77.6 - - - +
80Y LEU* 1.3 62.8 + - - +
95Y LEU* 3.6 26.3 - - + +
96Y THR* 3.2 12.8 - - - +
97Y GLY* 3.7 17.3 - - - +
134Y ALA* 4.3 12.9 + - - +
139Y THR* 4.4 8.1 - - - +
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Residues in contact with LEU 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y LEU* 3.1 28.9 - - + +
47Y PHE* 4.7 7.0 - - + -
70Y ALA* 4.0 29.4 - - + -
73Y PHE* 4.2 20.9 - - + +
78Y MET* 4.7 8.1 - - + +
79Y ARG* 1.3 85.3 - - - +
81Y SER* 1.3 62.4 + - - +
82Y PHE* 4.1 19.3 - - + -
93Y LEU* 4.0 7.3 - - - +
94Y PRO 3.5 3.1 - - - +
95Y LEU* 3.2 3.7 - - - -
96Y THR 2.8 29.9 + - - +
99Y ARG* 4.8 4.3 - - - +
102Y ILE* 3.7 31.9 - - + -
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Residues in contact with SER 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y LEU 3.0 6.3 + - - +
46Y TYR* 3.7 15.7 - - - -
47Y PHE* 2.9 26.9 + - - +
80Y LEU* 1.3 75.8 - - - +
82Y PHE* 1.3 71.4 + - - +
83Y ILE* 4.3 2.3 - - - +
91Y ILE* 4.4 0.9 - - - +
93Y LEU* 2.7 21.2 + - - -
95Y LEU* 3.5 14.6 - - - -
130Y GLN* 2.9 29.6 + - - -
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Residues in contact with PHE 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Y PHE* 3.8 23.3 - + + -
49Y LEU* 5.2 1.1 - - + -
66Y VAL* 3.6 17.7 - - + -
70Y ALA* 4.7 1.8 - - + -
80Y LEU* 4.1 22.0 - - + -
81Y SER* 1.3 81.9 + - - +
83Y ILE* 1.3 63.2 + - - +
91Y ILE* 3.7 1.7 - - - -
92Y ILE* 2.9 34.5 + - + -
93Y LEU* 3.0 42.1 + - + +
102Y ILE* 3.8 6.5 - - + -
105Y GLY* 3.7 23.3 - - - -
106Y LEU* 3.6 35.2 - - + -
109Y LEU* 3.7 21.5 - - + -
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Residues in contact with ILE 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Y TYR* 4.7 5.8 - - + -
47Y PHE* 2.6 17.5 + - - +
48Y VAL* 4.0 11.2 - - + -
49Y LEU* 2.7 37.4 + - - +
81Y SER* 4.3 7.9 - - - +
82Y PHE* 1.3 78.4 - - - +
84Y VAL* 1.3 68.3 + - - +
90Y THR 3.5 12.3 - - - +
91Y ILE* 4.4 9.0 - - + -
123Y GLY* 3.8 27.6 - - - +
126Y LEU* 4.0 10.3 - - + -
127Y ALA* 3.4 44.2 - - + +
130Y GLN* 4.1 9.6 - - - +
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Residues in contact with VAL 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LEU* 3.3 7.2 - - + +
51Y LYS* 4.0 20.6 - - + -
59Y TRP* 4.1 17.5 - - + -
83Y ILE* 1.3 80.7 - - - +
85Y PHE* 1.3 59.8 + - - +
88Y GLN 4.0 0.2 - - - +
89Y ALA* 3.3 2.9 - - - -
90Y THR* 2.8 52.3 + - - +
92Y ILE* 3.7 22.2 - - + -
109Y LEU* 3.7 28.0 - - + -
112Y VAL* 4.5 8.7 - - + -
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Residues in contact with PHE 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Y VAL* 3.8 30.7 - - + -
49Y LEU 2.9 16.7 + - - -
50Y ASP* 3.5 34.5 - - + -
51Y LYS* 2.9 29.4 + - - -
52Y SER 3.9 0.3 + - - -
84Y VAL* 1.3 75.8 - - - +
86Y SER* 1.3 61.3 + - - +
88Y GLN 3.2 10.8 - - - +
89Y ALA* 4.2 9.9 - - + -
118Y THR* 3.7 22.2 - - + -
119Y TYR 3.6 18.2 - - - +
120Y ILE* 3.5 50.9 - - + -
123Y GLY* 4.3 4.3 - - - +
146Y LEU 4.6 0.4 - - - -
147Y THR* 4.5 0.7 - - - -
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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