Contacts of the strand formed by residues 67 - 72 (chain B) in PDB entry 1T6S
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 GLY 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PRO* 3.7 19.3 - - - -
23B VAL 3.7 8.5 - - - -
24B ASN* 4.5 0.9 - - - -
63B ALA* 4.6 0.4 - - - -
64B ILE 2.9 33.2 + - - +
65B ALA 3.2 2.0 + - - -
66B GLY* 1.3 79.6 - - - +
68B TYR* 1.3 62.7 + - - -
69B ARG* 3.1 7.8 + - - -
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 4.0 15.5 - - + +
19B SER* 4.7 0.5 + - - -
22B PRO* 3.4 0.7 - - - +
23B VAL* 2.9 45.5 + - - +
24B ASN* 5.2 0.7 - - - -
25B LEU* 5.3 2.5 - - + -
28B LEU* 4.6 4.7 - - + -
38B PRO 4.8 1.7 + - - -
41B LEU* 3.6 28.7 - - + +
42B GLN* 2.7 44.4 + - - +
45B VAL* 3.7 20.4 - - + -
61B ILE* 3.8 25.8 - - + -
62B HIS 3.3 4.0 - - - -
63B ALA* 3.6 23.2 - - + +
66B GLY* 5.0 7.4 - - - -
67B GLY* 1.3 74.0 - - - -
69B ARG* 1.3 63.8 + - - +
414B NO3 3.7 6.5 - - - -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.3 21.2 + - - +
16B ILE* 4.0 11.2 - - - -
19B SER* 5.3 3.1 - - - +
21B GLU 5.5 0.4 - - - -
22B PRO* 3.1 42.9 - - + +
61B ILE* 4.3 1.5 - - - +
62B HIS* 2.9 41.5 + - - +
64B ILE* 3.0 54.6 + - - +
67B GLY 3.1 16.2 + - - -
68B TYR* 1.3 76.4 - - - +
70B PHE* 1.3 71.9 + - - +
71B LEU* 3.9 13.8 + - + +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 4.0 9.2 - - + -
16B ILE* 3.8 12.2 + - + +
17B PHE* 3.6 52.5 - + + -
52B TYR* 3.3 36.6 - + - -
59B PHE* 3.5 40.4 - + + -
60B ARG 3.3 10.8 - - - -
61B ILE* 3.5 19.5 - - + -
69B ARG* 1.3 76.4 - - - +
71B LEU* 1.3 72.6 + - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 4.2 22.9 - - + +
138A ARG* 3.8 11.9 - - - +
139A GLY* 3.5 32.1 - - - +
59B PHE* 3.3 3.7 - - - -
60B ARG* 2.9 30.8 + - - +
62B HIS* 3.5 36.5 + - + +
64B ILE* 5.6 2.7 - - + -
69B ARG* 3.9 17.9 - - + +
70B PHE* 1.3 90.0 - - - +
72B THR* 1.3 67.1 + - - +
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ARG 5.3 2.4 - - - +
58B THR* 3.4 17.5 - - - +
59B PHE* 4.1 9.6 - - + +
62B HIS* 5.5 1.5 + - - -
71B LEU* 1.3 80.8 - - - +
73B GLU* 1.3 68.9 + - - +
74B PRO* 3.7 1.9 - - - +
76B PHE* 5.4 4.7 - - - -
80B VAL* 3.6 32.1 - - + +
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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