Contacts of the strand formed by residues 424 - 431 (chain A) 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 GLN 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A ILE* 1.3 83.8 - - - +
425A TYR* 1.3 83.1 + - - +
426A SER* 4.5 5.4 - - - -
426D SER* 4.0 7.1 - - - -
427D GLY* 3.1 37.2 - - - +
428D GLU* 4.2 11.2 - - + +
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Residues in contact with TYR 425 (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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231A TYR* 5.0 0.9 + - - -
347A PRO* 3.9 22.5 - - + +
423A ILE* 3.7 38.5 - - + +
424A GLN* 1.3 81.7 - - - +
426A SER* 1.3 64.2 + - - +
44B VAL* 4.6 5.3 - - + +
53B GLN* 6.1 0.4 - - - -
44C VAL* 4.4 19.3 - - + +
47C ARG 3.7 21.3 - - - -
48C GLY* 3.9 12.3 - - - -
49C PRO* 3.7 23.6 - - + +
425D TYR 4.6 0.2 - - - -
426D SER* 3.2 3.1 - - - -
427D GLY 2.9 33.4 + - - +
429D VAL* 3.4 29.8 - - + -
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Residues in contact with SER 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLN* 4.5 5.8 - - - -
425A TYR* 1.3 78.6 - - - +
427A GLY* 1.3 57.8 + - - +
44C VAL* 4.8 2.4 + - - +
45C GLY* 4.3 10.0 - - - -
46C PRO* 5.4 1.6 - - - +
424D GLN* 3.0 17.5 + - - -
425D TYR 3.4 7.4 - - - -
426D SER* 3.8 10.2 - - - -
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Residues in contact with GLY 427 (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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426A SER* 1.3 75.6 - - - +
428A GLU* 1.3 66.0 + - - -
429A VAL 3.8 0.2 + - - -
44C VAL* 3.9 6.5 - - - +
45C GLY* 4.0 12.3 - - - -
46C PRO* 5.7 0.7 - - - -
424D GLN* 3.1 18.3 - - - +
425D TYR* 2.9 29.6 + - - +
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Residues in contact with GLU 428 (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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427A GLY* 1.3 73.0 - - - -
429A VAL* 1.3 61.3 + - - +
430A ARG* 3.2 33.8 + - + -
432A PHE* 3.3 11.5 - - + -
43C THR 3.3 0.3 - - - +
45C GLY 3.0 20.9 + - - +
422D SER* 3.7 24.8 - - - +
423D ILE 3.4 16.4 - - - +
424D GLN* 3.4 13.3 + - + +
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Residues in contact with VAL 429 (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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428A GLU* 1.3 70.2 - - - +
430A ARG* 1.3 59.7 + - - +
44B VAL* 5.0 0.2 - - + -
49B PRO* 4.3 2.0 - - + -
42C ILE* 3.4 19.5 - - + +
43C THR 3.4 4.5 - - - -
44C VAL* 4.1 17.0 - - + -
51C LEU* 3.4 35.4 - - + -
53C GLN* 3.7 17.3 - - - +
421D HIS 4.7 2.9 - - - +
422D SER* 4.2 12.3 + - - -
423D ILE 3.1 12.5 + - - +
425D TYR* 3.3 33.2 - - + -
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Residues in contact with ARG 430 (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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428A GLU* 3.2 30.8 + - + -
429A VAL* 1.3 75.2 - - - +
431A ARG* 1.3 82.9 + - - +
432A PHE* 3.3 58.1 + - + +
433A ASN 5.2 0.4 - - - +
42C ILE* 4.1 7.4 - - - -
43C THR 3.0 24.9 + - - +
419D LEU* 5.7 7.3 - - - +
420D GLU* 6.1 0.2 - - - -
422D SER* 3.4 22.5 + - - +
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Residues in contact with ARG 431 (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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159A ILE* 4.2 8.1 - - - +
430A ARG* 1.3 93.8 + - - +
432A PHE* 1.3 64.0 + - - +
433A ASN* 3.7 1.9 + - - +
35C VAL* 5.9 0.2 - - - -
37C ASP* 3.5 49.9 + - + +
40C ASN* 2.8 39.9 + - + +
41C VAL* 3.4 7.2 - - - +
42C ILE* 3.6 18.6 - - + +
54C ASP* 3.0 39.5 + - - +
56C VAL* 3.4 16.2 - - - +
419D LEU* 4.8 6.9 - - + +
420D GLU* 2.9 40.0 + - - +
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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