Contacts of the strand formed by residues 98 - 102 (chain G) in PDB entry 6D6Q
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 98 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G VAL* 3.8 16.9 - - - +
66G VAL* 3.8 18.4 + - - +
88G HIS* 3.6 10.1 - - - -
89G LYS 3.3 12.8 - - - -
90G GLU* 4.3 4.9 - - - -
91G PRO* 4.3 3.9 - - - +
96G GLY 3.3 6.2 + - - +
97G GLY* 1.3 75.0 - - - +
99G VAL* 1.3 64.4 - - - +
100G TYR* 5.3 0.4 - - - -
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Residues in contact with VAL 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G VAL* 3.2 28.5 - - + -
68G GLY* 5.4 2.9 - - - +
88G HIS* 2.6 28.5 + - - -
89G LYS* 2.9 64.8 + - + +
90G GLU* 5.0 0.9 - - - -
91G PRO* 5.9 0.9 - - + -
98G GLY* 1.3 76.7 - - - +
100G TYR* 1.3 72.9 + - - +
101G TRP* 3.4 11.6 - - + -
66L LEU* 5.0 3.6 - - + +
67L CYS* 4.4 15.0 - - + +
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Residues in contact with TYR 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ALA* 4.5 29.0 + - + +
21G ARG* 5.3 9.4 + - - +
24G LEU* 5.4 2.2 - - + -
34G LEU* 5.7 2.5 - - + -
36G LEU* 4.9 24.0 - - + +
37G PRO* 5.1 5.7 - - - +
65G VAL* 5.3 10.5 - - + -
66G VAL 3.9 9.2 + - - +
68G GLY* 3.1 23.0 + - - -
71G LEU* 3.9 19.3 - - + -
78G LEU* 4.6 15.5 - - + -
86G LEU* 4.9 14.6 - - + -
87G ARG 3.4 7.2 - - - -
88G HIS* 3.0 51.1 + + + -
98G GLY 5.3 0.4 - - - -
99G VAL* 1.3 78.6 - - - +
101G TRP* 1.3 70.3 + - - +
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Residues in contact with TRP 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G GLY* 4.3 4.7 - - - -
69G PRO* 3.6 23.6 - - + -
70G GLY 5.5 0.2 - - - +
71G LEU* 4.3 7.1 - - - +
86G LEU* 3.1 8.3 - - - +
87G ARG* 2.9 66.1 + - + +
88G HIS 3.2 38.6 - - - -
89G LYS* 3.3 20.0 - - + -
99G VAL* 3.4 15.0 - - + -
100G TYR* 1.3 100.7 - - - +
102G VAL* 1.3 77.1 + - - +
103G ASP* 4.2 4.3 - - - +
208G ARG* 6.3 1.7 - - - +
64L PHE* 5.4 4.0 - + - -
67L CYS* 3.2 39.9 - - + -
68L GLU* 5.1 10.0 + - + -
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Residues in contact with VAL 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G VAL* 4.0 20.9 - - + -
69G PRO* 4.9 1.0 - - - +
70G GLY* 3.6 32.4 - - - +
71G LEU* 4.4 12.3 - - + -
80G VAL* 4.9 0.7 - - + -
82G LYS* 4.2 19.7 - - + +
84G GLY* 4.3 12.6 - - - -
85G ARG 4.3 3.8 - - - -
86G LEU* 3.8 18.4 - - + -
101G TRP* 1.3 87.6 - - - +
103G ASP* 1.3 58.9 + - - +
104G SER* 2.9 16.9 + - - +
64L PHE* 4.3 12.0 - - - -
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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
------------------------------------------------------------
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