Contacts of the strand formed by residues 424 - 431 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A SER* 3.0 26.9 + - - -
427A GLY* 3.1 30.6 - - - +
428A GLU* 3.4 14.2 + - + +
423D ILE* 1.3 83.2 - - - +
425D TYR* 1.3 77.8 + - - +
426D SER* 4.0 5.8 + - - +
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Residues in contact with TYR 425 (chain D).
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* 3.4 1.6 - - - -
427A GLY 2.9 34.6 + - - +
429A VAL* 3.3 33.7 - - + -
44B VAL* 4.3 20.6 - - + +
47B ARG 3.7 17.3 - - - -
48B GLY* 3.8 13.5 - - - -
49B PRO* 3.7 23.9 - - + +
44C VAL* 4.3 3.1 - - + +
53C GLN* 5.3 2.4 + - - -
231D TYR* 4.8 1.3 + - - -
347D PRO* 3.9 20.0 - - + +
423D ILE* 3.3 52.6 - - + +
424D GLN* 1.3 80.5 + - - +
426D SER* 1.3 62.0 + - - +
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Residues in contact with SER 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLN* 4.0 5.8 - - - -
425A TYR 3.2 12.8 - - - -
426A SER* 3.8 17.0 - - - -
44B VAL* 4.6 6.0 + - - +
45B GLY* 4.0 10.9 - - - -
46B PRO* 5.3 1.4 - - - +
424D GLN* 4.0 5.8 + - - +
425D TYR* 1.3 77.2 - - - +
427D GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A GLN* 3.1 20.6 - - - +
425A TYR* 2.9 30.0 + - - +
44B VAL* 4.3 5.2 - - - +
45B GLY* 4.3 8.7 - - - -
46B PRO* 5.7 1.3 - - - -
426D SER* 1.3 75.0 - - - +
428D GLU* 1.3 65.1 + - - -
429D VAL 3.8 0.7 + - - -
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Residues in contact with GLU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A SER* 3.4 25.7 + - - +
423A ILE 3.4 11.4 - - - +
424A GLN* 4.2 12.5 - - + +
45B GLY 3.0 20.6 + - - -
427D GLY* 1.3 72.8 - - - -
429D VAL* 1.3 60.8 + - - +
430D ARG* 2.9 41.2 + - + +
432D PHE* 3.2 17.9 - - + -
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Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A HIS 4.8 1.4 - - - +
422A SER* 3.4 16.6 - - - -
423A ILE 3.0 14.4 + - - +
425A TYR* 3.4 31.6 - - + -
42B ILE* 3.5 14.4 - - + +
43B THR 3.4 4.3 - - - +
44B VAL* 3.8 27.8 - - + -
51B LEU* 3.3 32.5 - - + -
53B GLN* 3.8 14.4 - - - +
44C VAL* 5.2 0.7 - - + -
49C PRO* 4.8 2.5 - - + -
428D GLU* 1.3 69.1 - - - +
430D ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A GLU* 5.9 1.3 - - - +
422A SER* 3.7 17.9 - - - -
42B ILE* 3.9 9.8 - - - +
43B THR 3.1 19.4 + - - -
428D GLU* 2.9 29.4 + - + -
429D VAL* 1.3 77.4 - - - +
431D ARG* 1.3 84.3 + - - +
432D PHE* 3.1 60.7 + - + +
433D ASN 5.0 1.2 - - - +
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Residues in contact with ARG 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A LEU* 4.0 9.4 - - + +
420A GLU* 2.8 39.2 + - - +
37B ASP* 3.6 46.5 + - + +
40B ASN* 2.7 39.8 + - + +
41B VAL* 3.3 10.7 - - - +
42B ILE* 3.6 18.5 - - + +
54B ASP* 2.9 39.3 + - - +
55B VAL 5.1 0.2 - - - +
56B VAL* 3.7 16.5 - - - +
159D ILE* 4.2 7.1 - - - +
430D ARG* 1.3 88.8 + - - +
432D PHE* 1.3 63.2 + - - +
433D ASN 3.8 1.2 + - - -
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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