Contacts of the strand formed by residues 141 - 145 (chain H) in PDB entry 3GTL
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 141 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A THR* 5.0 8.3 - - + +
566A ILE* 4.8 16.8 - - + -
59H ILE* 3.2 37.6 + - - +
60H ALA* 4.4 3.4 + - + -
61H SER* 4.0 8.1 - - - -
62H SER* 3.7 36.9 + - - -
63H LEU 3.7 21.3 - - - -
96H VAL* 5.0 9.0 - - + -
97H MET 3.5 9.9 - - - +
98H TYR* 3.9 37.3 - + + +
118H PHE* 4.3 2.0 - - - -
139H ASN* 5.1 5.6 - - - -
140H ALA* 1.3 83.0 - - - +
142H LEU* 1.3 63.7 + - - +
143H LEU* 4.2 9.0 - - + -
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Residues in contact with LEU 142 (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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40H LEU* 3.8 21.5 - - + -
42H ILE* 5.6 0.7 - - + -
57H VAL* 3.7 15.7 - - + -
58H THR 3.3 21.5 - - - +
59H ILE* 4.3 1.3 - - + -
95H TYR 4.2 0.7 - - - +
96H VAL* 3.3 6.1 - - - +
97H MET* 2.9 44.6 + - + +
118H PHE* 3.5 34.1 - - + -
123H MET* 3.5 31.4 - - + -
141H TYR* 1.3 79.5 - - - +
143H LEU* 1.3 67.0 - - - +
144H ILE* 4.9 8.7 - - + -
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Residues in contact with LEU 143 (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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56H THR 3.4 1.2 - - - +
57H VAL* 3.3 5.9 - - - -
58H THR* 2.8 46.7 + - + -
59H ILE 3.3 26.9 - - - +
60H ALA* 4.5 5.8 - - + -
63H LEU 6.0 4.3 - - - +
90H ALA* 3.3 19.3 - - + +
91H ASP* 4.1 2.9 - - + -
93H TYR* 3.1 43.4 - - + -
95H TYR 3.9 2.9 - - - -
96H VAL* 3.5 27.8 - - + -
141H TYR* 4.2 5.8 - - + -
142H LEU* 1.3 78.0 - - - +
144H ILE* 1.3 62.2 + - - +
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Residues in contact with ILE 144 (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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40H LEU* 3.9 16.2 - - + -
42H ILE* 3.8 31.0 - - + -
47H PHE* 3.7 31.0 - - + -
55H LEU* 3.9 33.7 - - + -
56H THR 3.2 3.8 - - - -
57H VAL* 3.9 14.4 - - + -
93H TYR* 3.3 5.9 - - - +
94H ASP 3.3 12.1 + - - -
95H TYR* 2.9 32.2 + - + +
142H LEU* 4.2 8.5 - - + -
143H LEU* 1.3 74.9 - - - +
145H ARG* 1.3 70.1 + - - +
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Residues in contact with ARG 145 (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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7H ASP* 5.2 2.4 + - - -
47H PHE* 5.2 0.2 - - - -
55H LEU* 3.7 3.8 - - - -
56H THR* 3.1 58.3 + - - +
92H ASP* 4.0 22.6 - - - +
93H TYR* 3.3 48.0 + - + -
94H ASP* 3.6 18.2 - - - +
144H ILE* 1.3 84.6 - - - +
146H ARG* 1.3 94.2 + - + +
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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