Contacts of the strand formed by residues 78 - 87 (chain B) in PDB entry 1DGB
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 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ALA 3.7 0.4 + - - -
77B LYS* 1.3 78.6 - - - +
79B ALA* 1.3 58.6 + - - +
112B ARG* 3.3 17.1 - - - +
113B PHE 2.7 15.9 - - - -
114B SER* 3.8 1.1 - - - -
124B ASP* 5.6 2.7 - - - -
209B HIS* 5.4 2.5 - - - -
262B ILE* 3.8 14.3 - - - +
325B TYR* 2.7 29.4 + - - -
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Residues in contact with ALA 79 (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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78B GLY* 1.3 75.2 - - - +
80B GLY* 1.3 57.9 + - - +
112B ARG* 3.1 4.9 - - - +
113B PHE* 2.7 34.7 + - + +
209B HIS* 4.0 26.0 + - + +
262B ILE* 3.9 27.4 - - + -
265B LEU* 4.2 11.7 - - + -
325B TYR* 4.6 3.4 - - - -
329B VAL* 4.0 6.1 - - - -
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Residues in contact with GLY 80 (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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79B ALA* 1.3 77.0 - - - +
81B ALA* 1.3 64.6 + - - +
82B PHE* 6.2 0.2 - - - -
111B VAL 3.3 9.4 - - - -
112B ARG* 4.3 0.4 - - - -
113B PHE* 5.4 0.4 - - - -
265B LEU* 3.9 8.6 - - - +
321B ASN* 5.1 0.7 - - - +
322B PRO* 3.4 23.0 - - - +
325B TYR* 4.6 2.2 - - - -
329B VAL* 3.7 25.8 - - - +
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Residues in contact with ALA 81 (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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80B GLY* 1.3 76.3 - - - +
82B PHE* 1.3 75.9 + - - +
111B VAL* 3.0 30.5 + - - +
113B PHE* 5.3 0.4 - - + -
265B LEU* 3.9 8.5 - - + -
269B ILE* 3.7 22.7 - - + -
318B LEU* 3.9 23.3 - - + -
320B ARG 3.5 11.7 - - - +
321B ASN* 5.2 0.7 - - - +
322B PRO* 4.3 2.0 - - - +
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 1.3 85.6 - - - +
83B GLY* 1.3 61.1 + - - +
109B ILE 3.5 15.0 - - - +
110B ALA* 3.8 20.9 - - + -
111B VAL 5.8 0.4 - - - -
137B TYR* 4.7 4.9 - + - -
318B LEU* 3.3 9.0 - - - -
319B ASN* 2.8 7.9 + - - -
320B ARG* 2.8 85.5 + - - +
322B PRO* 4.0 21.1 - - + -
328B GLU* 3.3 48.7 - - + -
329B VAL* 5.4 0.4 - - + -
332B ILE* 5.1 1.3 - - + -
375B VAL* 4.2 12.3 - - + -
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Residues in contact with GLY 83 (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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82B PHE* 1.3 79.4 - - - +
84B TYR* 1.3 65.4 + - - +
108B PRO* 3.6 5.2 - - - +
109B ILE* 2.8 27.4 + - - +
317B VAL 2.9 11.9 - - - -
319B ASN* 3.1 17.0 - - - -
320B ARG* 4.6 4.7 + - - +
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Residues in contact with TYR 84 (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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83B GLY* 1.3 77.3 - - - +
85B PHE* 1.3 71.9 + - - +
86B GLU* 3.8 26.3 + - + -
106B LYS* 3.9 31.2 + - + -
107B THR 3.2 17.5 - - - +
108B PRO* 4.4 2.0 - - + -
109B ILE* 3.2 10.6 - - - +
315B LYS* 3.9 0.4 - - + +
316B LEU 3.7 0.3 - - - -
317B VAL* 2.8 67.1 + - + +
319B ASN* 3.8 24.0 - - - -
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Residues in contact with PHE 85 (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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84B TYR* 1.3 77.1 - - - +
86B GLU* 1.3 65.9 - - - +
87B VAL* 3.9 12.1 - - + -
99B VAL* 3.8 39.9 - - + -
100B PHE* 4.1 19.3 - + - -
105B LYS 3.4 2.0 - - - +
106B LYS* 3.3 4.3 - - - -
107B THR* 2.9 34.3 + - - +
109B ILE* 3.8 7.2 - - + -
136B PHE* 3.6 24.5 - + + -
279B PHE* 3.9 29.2 - + + -
313B VAL* 4.1 13.5 - - + -
314B GLY* 4.1 0.9 - - - -
315B LYS 3.1 28.7 - - - -
316B LEU* 3.7 15.7 - - + -
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Residues in contact with GLU 86 (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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84B TYR* 3.8 20.0 + - + -
85B PHE* 1.3 77.1 - - - +
87B VAL* 1.3 72.3 + - - +
88B THR* 3.5 9.2 + - + +
104B GLY* 4.3 17.7 - - - +
105B LYS 3.4 7.9 - - - +
106B LYS* 3.5 26.8 - - + -
314B GLY* 3.1 4.6 - - - -
315B LYS* 2.9 40.5 + - + +
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Residues in contact with VAL 87 (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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85B PHE* 3.9 10.3 - - + -
86B GLU* 1.3 75.7 - - - +
88B THR* 1.3 59.0 + - - +
89B HIS 3.2 26.5 - - - +
90B ASP* 5.5 0.4 - - - -
99B VAL 3.2 27.4 - - - +
100B PHE* 3.9 18.6 - - + +
102B HIS 3.4 26.5 - - - +
103B ILE* 3.4 8.4 - - - +
104B GLY* 2.7 28.7 + - - +
105B LYS* 3.2 15.1 + - + +
313B VAL* 3.8 9.0 - - + +
314B GLY* 4.3 0.9 - - - -
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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