Contacts of the strand formed by residues 78 - 87 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ALA 3.4 6.1 + - - -
77A LYS* 1.3 80.3 - - - +
79A ALA* 1.3 59.4 + - - +
112A ARG* 3.6 14.0 - - - +
113A PHE 2.9 14.1 - - - -
114A SER* 3.9 1.3 - - - -
124A ASP* 5.5 2.0 - - - -
209A HIS* 5.2 2.0 - - - -
262A ILE* 3.8 13.3 - - - +
325A TYR* 2.7 30.1 + - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY* 1.3 75.1 - - - +
80A GLY* 1.3 59.3 + - - +
112A ARG* 3.2 3.1 - - - +
113A PHE* 2.7 33.3 + - - +
209A HIS* 4.0 23.9 + - + +
262A ILE* 3.9 31.2 - - + -
265A LEU* 4.1 12.1 - - + -
325A TYR* 4.6 3.4 - - - -
329A VAL* 4.2 6.5 - - - -
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA* 1.3 77.4 - - - +
81A ALA* 1.3 62.7 + - - +
82A PHE* 5.0 0.7 - - - -
111A VAL 3.2 11.9 - - - -
112A ARG* 4.3 0.2 - - - -
113A PHE* 5.4 0.2 - - - -
265A LEU* 4.1 7.5 - - - +
321A ASN* 4.8 1.6 - - - +
322A PRO* 3.2 26.6 - - - +
325A TYR* 4.9 1.4 - - - -
329A VAL* 3.8 23.9 - - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 1.3 75.7 - - - +
82A PHE* 1.3 75.0 + - - +
111A VAL* 3.0 31.0 + - + +
113A PHE* 5.5 1.1 - - + -
265A LEU* 4.1 12.8 - - + +
269A ILE* 3.5 29.8 - - + -
318A LEU* 4.3 18.2 - - + -
320A ARG 3.5 5.6 - - - +
321A ASN* 4.9 0.9 - - - +
322A PRO* 4.7 0.9 - - - -
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 5.0 0.9 - - - -
81A ALA* 1.3 84.1 - - - +
83A GLY* 1.3 57.7 + - - +
109A ILE 3.6 7.2 - - - +
110A ALA* 3.9 27.6 - - + -
111A VAL 6.0 0.4 - - - -
137A TYR* 4.8 4.3 - + - -
318A LEU* 3.5 7.4 - - - +
319A ASN 2.9 6.1 + - - -
320A ARG* 2.6 90.3 + - + +
321A ASN 4.2 4.9 - - - -
322A PRO* 3.9 20.9 - - + -
328A GLU* 3.5 47.8 - - + -
329A VAL* 5.3 1.1 - - + -
332A ILE* 5.6 0.4 - - + -
375A VAL* 4.0 14.6 - - + -
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 1.3 77.1 - - - +
84A TYR* 1.3 65.4 + - - +
108A PRO* 3.7 5.2 - - - +
109A ILE* 3.0 26.5 + - - +
317A VAL 3.1 12.6 - - - -
318A LEU* 4.0 2.0 - - - +
319A ASN* 3.5 17.0 - - - -
320A ARG* 4.7 5.7 + - - +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY* 1.3 75.1 - - - +
85A PHE* 1.3 71.6 + - - +
86A GLU* 3.7 28.0 + - + -
106A LYS* 4.2 24.1 + - + -
107A THR 3.3 17.0 - - - +
108A PRO* 4.5 1.6 - - + -
109A ILE* 3.5 11.5 - - - +
315A LYS 3.7 0.3 - - - +
317A VAL* 2.8 67.0 + - + +
319A ASN* 3.7 27.1 - - - -
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Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR* 1.3 74.5 - - - +
86A GLU* 1.3 63.0 + - - +
87A VAL* 3.5 30.7 - - + -
99A VAL* 3.7 30.3 - - + -
100A PHE* 4.2 18.6 - + - -
105A LYS 3.6 1.7 - - - +
106A LYS* 3.0 5.7 - - - +
107A THR* 2.7 39.5 + - - +
109A ILE* 3.9 5.1 - - + +
136A PHE* 3.8 23.1 - + + -
279A PHE* 4.0 29.4 - + + -
313A VAL* 4.3 6.5 - - + -
314A GLY* 4.0 13.7 - - - -
315A LYS 3.2 16.6 - - - -
316A LEU* 3.7 16.2 - - + -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR* 3.7 24.8 + - + -
85A PHE* 1.3 78.4 - - - +
87A VAL* 1.3 74.9 + - - +
88A THR* 3.9 9.1 - - + +
104A GLY* 4.4 11.0 - - - +
105A LYS 3.4 4.7 - - - +
106A LYS* 3.3 33.0 + - + -
314A GLY* 3.0 2.9 - - - -
315A LYS* 2.7 45.2 + - + +
317A VAL* 5.8 0.2 - - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.5 14.6 - - + -
86A GLU* 1.3 77.3 - - - +
88A THR* 1.3 63.8 + - - +
89A HIS 3.2 23.1 - - - +
99A VAL 3.3 27.1 - - - +
100A PHE* 4.1 14.1 - - + +
102A HIS 3.4 27.1 - - - +
103A ILE* 3.7 9.1 - - + +
104A GLY* 2.9 24.0 + - - +
105A LYS* 3.0 13.7 + - + +
313A VAL* 3.7 9.0 - - + +
314A GLY* 4.1 1.3 - - - -
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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