Contacts of the strand formed by residues 311 - 320 (chain C) in PDB entry 1DGH
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ILE* 4.5 10.8 - - + -
94C TYR* 4.2 19.1 - - + +
280C TYR* 3.1 3.5 - - - -
281C ILE* 2.9 45.7 + - + +
283C VAL* 3.9 33.2 - - + +
309C PRO* 3.6 17.3 - - + +
310C LEU* 1.3 73.6 - - - +
312C PRO* 1.3 78.4 - - + +
313C VAL* 3.6 1.9 - - - +
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Residues in contact with PRO 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C THR* 5.2 0.2 - - - +
89C HIS* 3.3 50.8 - - + +
91C ILE* 4.2 2.4 - - - +
278C THR* 5.4 5.8 - - + -
279C PHE 3.8 0.7 - - - +
280C TYR* 3.5 25.1 - - + -
310C LEU 3.7 7.6 - - - +
311C ILE* 1.3 97.0 - - + +
313C VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 4.3 4.0 - - + -
87C VAL* 3.7 6.8 - - + +
88C THR* 2.8 25.0 + - - -
89C HIS* 3.0 12.1 + - - +
91C ILE* 3.7 30.3 - - + -
100C PHE* 4.0 22.0 - - + -
279C PHE* 2.7 26.5 + - + +
280C TYR 4.0 1.6 - - - -
281C ILE* 3.8 31.4 - - + -
311C ILE 3.6 11.2 - - - +
312C PRO* 1.3 80.0 - - - +
314C GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PHE* 4.0 7.0 - - - -
86C GLU 3.0 14.6 - - - -
88C THR* 3.1 12.6 + - - -
278C THR* 3.7 6.9 - - - +
279C PHE* 2.7 35.9 + - - +
313C VAL* 1.3 82.2 - - - +
315C LYS* 1.3 64.0 + - - +
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TYR 3.8 0.5 - - - +
85C PHE* 3.1 10.7 - - - -
86C GLU* 2.8 44.1 + - + +
88C THR* 4.1 15.5 - - + -
239C ASP* 2.8 27.8 + - - +
276C SER* 5.0 4.5 - - - -
277C TRP 3.4 14.1 - - - +
278C THR* 3.0 25.8 + - - +
279C PHE* 4.5 0.4 - - - +
314C GLY* 1.3 76.3 - - - +
316C LEU* 1.3 62.4 + - - +
317C VAL* 4.0 14.1 - - + +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TYR 3.6 1.3 - - - -
85C PHE* 3.9 23.6 - - + -
109C ILE* 3.9 22.7 - - + -
111C VAL* 6.2 0.9 - - + -
132C PHE* 4.7 4.9 - - + -
134C VAL* 4.2 21.5 - - + -
136C PHE* 4.3 7.0 - - + -
236C TYR* 3.7 44.2 - - + -
275C PRO 3.9 0.2 - - - +
276C SER* 3.1 8.8 - - - -
277C TRP* 2.9 44.1 + - + +
279C PHE* 4.0 13.7 - - + -
315C LYS* 1.3 73.4 - - - +
317C VAL* 1.3 59.7 + - - +
318C LEU* 4.3 1.1 - - + -
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY* 3.0 4.5 - - - -
84C TYR* 2.8 82.4 + - + +
86C GLU* 5.9 0.4 - - - +
109C ILE* 4.3 0.6 - - - +
274C TYR* 4.4 15.3 - - + +
275C PRO 3.7 7.6 - - - +
276C SER* 4.2 12.8 - - - -
315C LYS* 4.5 13.5 - - + -
316C LEU* 1.3 79.3 - - - +
318C LEU* 1.3 73.1 + - - +
319C ASN* 4.7 4.3 - - + +
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 3.8 21.8 - - + -
82C PHE* 3.5 15.9 - - - +
109C ILE* 3.8 21.8 - - + -
111C VAL* 3.8 20.0 - - + -
113C PHE* 3.8 27.6 - - + -
132C PHE* 5.5 0.7 - - + -
265C LEU* 5.0 1.1 - - + -
269C ILE* 3.9 5.9 - - + +
274C TYR* 3.3 19.0 - - - +
275C PRO* 3.2 29.6 + - + +
277C TRP* 3.8 25.8 - - + -
316C LEU* 4.3 1.1 - - + -
317C VAL* 1.3 79.6 - - - +
319C ASN* 1.3 59.0 + - - +
320C ARG 3.8 0.9 - - - -
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Residues in contact with ASN 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE 2.9 9.8 + - - +
83C GLY* 3.6 10.5 - - - -
84C TYR* 3.7 27.3 - - - -
269C ILE* 3.7 9.4 - - - +
274C TYR* 3.6 43.0 + - + -
317C VAL* 4.7 2.7 - - + +
318C LEU* 1.3 73.3 - - - +
320C ARG* 1.3 67.2 + - - +
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Residues in contact with ARG 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 3.6 3.3 - - - +
82C PHE* 2.8 82.4 + - - +
83C GLY* 5.0 4.8 + - - +
269C ILE* 3.7 7.2 - - - +
318C LEU 3.8 0.6 - - - -
319C ASN* 1.3 85.7 + - - +
321C ASN* 1.3 73.6 + - - +
323C VAL* 5.9 5.3 - - + +
328C GLU* 4.7 6.5 + - - -
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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