Contacts of the strand formed by residues 311 - 320 (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 ILE 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ILE* 4.6 11.0 - - + -
93A LYS* 5.6 2.5 - - - +
94A TYR* 4.2 20.6 - - + +
280A TYR* 3.1 4.3 - - - -
281A ILE* 2.7 50.7 + - + +
283A VAL* 3.8 35.7 - - + +
309A PRO* 3.7 10.1 - - + +
310A LEU* 1.3 77.9 - - - +
312A PRO* 1.3 78.9 - - + +
313A VAL* 3.5 3.3 - - - +
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Residues in contact with PRO 312 (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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88A THR* 5.2 0.4 - - - +
89A HIS* 3.2 50.9 - - + +
91A ILE* 4.3 2.6 - - - +
278A THR* 5.5 4.3 - - + -
279A PHE 3.9 0.4 - - - +
280A TYR* 3.5 25.0 - - + -
310A LEU 3.9 6.3 - - - +
311A ILE* 1.3 96.0 - - + +
313A VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 313 (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* 4.3 5.2 - - + -
87A VAL* 3.7 4.6 - - + +
88A THR* 2.7 31.7 + - - -
89A HIS* 2.9 16.2 + - - +
91A ILE* 3.4 44.9 - - + -
100A PHE* 4.1 15.7 - - + -
279A PHE* 2.8 27.2 + - + +
280A TYR 4.3 0.2 - - - -
281A ILE* 3.9 20.0 - - + +
311A ILE 3.5 11.9 - - - +
312A PRO* 1.3 79.9 - - - +
314A GLY* 1.3 51.2 + - - +
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Residues in contact with GLY 314 (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* 4.0 7.4 - - - -
86A GLU 3.0 14.1 - - - -
87A VAL* 4.1 0.7 - - - -
88A THR* 3.3 11.9 + - - -
278A THR* 3.6 6.8 - - - +
279A PHE* 2.7 35.9 + - - +
313A VAL* 1.3 82.6 - - - +
315A LYS* 1.3 62.7 + - - +
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Residues in contact with LYS 315 (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 0.9 - - - +
85A PHE* 3.2 10.1 - - - -
86A GLU* 2.7 44.1 + - + +
88A THR* 4.2 13.7 - - + -
239A ASP* 2.7 37.2 + - - +
276A SER* 4.4 8.7 + - - +
277A TRP 3.3 8.1 - - - +
278A THR* 3.5 17.0 + - + +
279A PHE* 4.4 0.4 - - - +
314A GLY* 1.3 77.3 - - - +
316A LEU* 1.3 61.8 + - - +
317A VAL* 4.0 13.4 - - + +
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Residues in contact with LEU 316 (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 3.8 0.4 - - - -
85A PHE* 3.7 25.4 - - + -
109A ILE* 3.9 23.8 - - + -
111A VAL* 6.2 0.4 - - + -
132A PHE* 4.9 5.4 - - + -
134A VAL* 4.4 13.2 - - + -
136A PHE* 4.2 13.2 - - + -
236A TYR* 3.7 42.2 - - + -
276A SER* 2.9 9.0 - - - -
277A TRP* 2.7 50.6 + - + +
279A PHE* 4.1 15.3 - - + -
315A LYS* 1.3 73.0 - - - +
317A VAL* 1.3 60.5 + - - +
318A LEU* 5.5 1.3 - - + -
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Residues in contact with VAL 317 (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* 3.1 2.3 - - - -
84A TYR* 2.8 79.3 + - + +
109A ILE* 3.9 1.3 - - - +
274A TYR* 4.4 14.1 - - + -
275A PRO 3.7 8.3 - - - +
276A SER* 4.1 10.8 - - - -
315A LYS* 4.5 14.6 - - + -
316A LEU* 1.3 78.2 - - - +
318A LEU* 1.3 77.3 + - - +
319A ASN* 4.7 4.3 - - + +
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Residues in contact with LEU 318 (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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81A ALA* 4.3 7.6 - - + -
82A PHE* 3.5 24.2 - - - +
83A GLY 4.0 1.3 - - - +
109A ILE* 4.1 4.9 - - + -
111A VAL* 3.7 31.4 - - + -
113A PHE* 4.1 25.8 - - + -
132A PHE* 5.6 0.9 - - + -
265A LEU* 5.0 1.6 - - + -
269A ILE* 3.8 13.0 - - + +
274A TYR* 3.0 21.9 - - - +
275A PRO* 3.1 27.8 + - + +
277A TRP* 3.9 25.8 - - + -
316A LEU* 5.5 0.7 - - + -
317A VAL* 1.3 82.7 - - - +
319A ASN* 1.3 61.1 + - - +
320A ARG 3.8 0.7 - - - -
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Residues in contact with ASN 319 (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 2.9 9.7 + - - +
83A GLY* 3.5 10.1 - - - -
84A TYR* 3.7 31.1 - - - -
269A ILE* 3.5 13.5 - - - +
274A TYR* 3.5 43.2 + - + -
317A VAL* 4.8 3.0 - - + +
318A LEU* 1.3 74.6 - - - +
320A ARG* 1.3 69.7 + - - +
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Residues in contact with ARG 320 (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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81A ALA* 3.4 1.7 - - - -
82A PHE* 2.6 98.1 + - - +
83A GLY* 4.7 5.3 + - - +
269A ILE* 3.7 5.4 - - - +
318A LEU 3.8 0.2 - - - -
319A ASN* 1.3 82.6 + - - +
321A ASN* 1.3 67.5 + - - +
323A VAL* 6.1 3.9 - - + +
328A GLU* 5.0 5.7 + - - -
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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