Contacts of the strand formed by residues 78 - 84 (chain E) 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 TYR 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67E GLY* 5.0 2.4 - - - -
68E THR 3.5 23.5 + - - -
69E PRO* 4.4 6.7 - - + -
70E LYS* 3.7 38.6 - - + +
77E GLY* 1.3 83.4 - - - +
79E LEU* 1.3 64.1 + - - +
80E GLU* 3.5 39.7 - - + -
121E LEU* 4.2 9.0 - - + +
124E LEU* 5.0 2.1 - - - +
132E CYS* 6.0 0.2 - - + -
133E TRP 3.8 3.2 + - - -
134E VAL* 3.2 39.0 - - + +
135E LEU* 3.0 25.0 + - - +
136E TYR* 4.1 11.0 + - - -
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Residues in contact with LEU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LYS* 5.2 1.2 + - - -
78E TYR* 1.3 77.2 - - - +
80E GLU* 1.3 69.6 + - - +
81E PHE* 3.9 19.5 - - + -
110E TYR* 4.1 11.6 - - - -
113E PHE* 3.7 36.6 - - + -
119E VAL* 4.4 19.5 - - + -
121E LEU* 3.5 31.4 - - + +
135E LEU* 3.5 31.9 - - + +
137E VAL* 5.1 4.3 - - + -
160E LEU* 5.0 7.6 - - + -
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Residues in contact with GLU 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ARG* 6.0 1.6 - - - +
70E LYS* 3.3 27.2 + - - -
78E TYR* 3.5 26.2 - - + -
79E LEU* 1.3 76.4 - - - +
81E PHE* 1.3 63.2 + - - +
110E TYR* 3.0 27.0 + - - +
135E LEU 2.9 7.8 + - - +
136E TYR* 3.8 30.3 - - + -
137E VAL* 2.9 30.6 + - - +
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Residues in contact with PHE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ARG* 5.3 0.9 - - - -
79E LEU* 3.9 22.0 - - + -
80E GLU* 1.3 76.8 - - - +
82E PHE* 1.3 63.7 + - - +
83E VAL* 5.2 0.9 - - + -
106E ALA* 4.3 12.1 - - + +
109E LEU* 3.4 52.0 - - + -
110E TYR* 3.3 41.6 + + + -
113E PHE* 3.3 44.4 - + + -
137E VAL* 3.3 39.3 - - + -
139E VAL* 5.3 1.1 - - + -
156E VAL* 4.4 6.5 - - + -
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Residues in contact with PHE 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B THR* 3.8 27.6 - - + -
85B ARG* 3.4 24.0 - - - +
87B ARG* 4.0 37.5 - - + -
88B ARG* 4.8 1.6 - - - -
89B PRO* 4.0 21.3 - - + -
90B HIS* 5.3 9.6 - + - -
81E PHE* 1.3 74.2 - - - +
83E VAL* 1.3 81.8 + - - +
84E ASP* 4.1 25.4 - - + -
106E ALA* 5.5 0.4 - - - -
137E VAL 2.9 7.1 + - - +
138E ASP* 3.5 9.6 - - + +
139E VAL* 2.9 26.1 + - - +
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Residues in contact with VAL 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E PHE* 5.1 3.4 - - + -
82E PHE* 1.3 97.4 - - - +
84E ASP* 1.3 64.9 + - - +
85E CYS 3.3 5.7 + - - +
102E GLY* 3.9 39.6 - - - +
105E ILE* 4.2 21.3 - - + -
106E ALA* 4.1 15.8 - - + +
109E LEU* 5.3 1.8 - - + -
139E VAL* 3.6 28.3 - - + +
141E LEU* 4.6 13.7 - - + -
152E ILE* 6.0 0.2 - - + -
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Residues in contact with ASP 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B SER* 3.5 20.1 + - - -
78B ALA* 5.0 2.7 - - - -
79B THR* 6.2 0.7 - - + -
89B PRO* 4.2 15.8 - - + +
90B HIS* 4.9 9.9 + - - -
125B GLN* 3.5 15.8 + - - +
82E PHE* 4.1 15.9 - - + -
83E VAL* 1.3 70.1 - - - +
85E CYS* 1.3 60.6 + - - +
86E SER* 3.0 15.1 + - - -
139E VAL 2.9 11.2 + - - +
140E LEU* 3.5 18.3 - - + +
141E LEU* 3.0 26.2 + - - +
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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