Contacts of the strand formed by residues 369 - 374 (chain B) in PDB entry 1HDZ
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 ARG 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B GLY* 4.8 0.4 - - - -
45B ILE 3.2 29.1 + - - +
46B CYS* 3.2 23.8 - - - +
47B GLY 4.2 0.4 - - - +
68B GLU* 2.7 26.6 + - - -
171B LEU* 3.6 26.8 - - + +
175B GLY* 3.2 31.7 - - - -
202B GLY* 4.0 20.0 - - - +
203B VAL* 3.9 1.4 - - - +
345B LEU* 2.8 25.5 + - + +
346B ILE* 3.5 5.7 - - + +
347B THR* 2.9 30.9 + - - +
348B HIS 3.5 1.9 + - - +
362B LEU* 5.7 0.8 - - - +
368B ILE* 1.3 73.7 + - - +
370B THR* 1.3 60.2 + - - +
371B VAL* 3.9 0.8 + - + -
377B NAD 2.8 33.1 + - - -
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Residues in contact with THR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL 3.8 0.2 - - - +
44B GLY* 3.5 2.9 - - - -
45B ILE* 3.0 45.5 + - + +
348B HIS* 3.2 23.6 - - + +
350B LEU* 3.9 29.2 - - + -
358B GLY* 4.2 14.6 + - - -
361B LEU* 4.2 1.4 - - + +
367B SER* 3.6 21.4 + - - -
368B ILE 4.1 2.0 + - - -
369B ARG* 1.3 73.1 - - - +
371B VAL* 1.3 71.5 + - - +
372B LEU* 4.1 2.9 + - + -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 4.1 15.7 - - + -
43B VAL 3.4 6.3 - - - +
44B GLY* 4.7 4.0 - - - -
167B GLU* 3.7 23.6 - - + +
170B CYS* 4.3 12.1 - - - -
171B LEU* 4.8 7.6 - - + -
346B ILE* 3.6 29.4 - - + -
348B HIS 2.8 9.6 + - - +
349B VAL* 3.1 19.7 - - + +
350B LEU 2.8 26.2 + - - -
369B ARG 4.9 0.9 - - - +
370B THR* 1.3 77.0 - - - +
372B LEU* 1.3 71.1 + - - +
373B THR* 4.5 3.4 - - + -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.4 4.9 - - - -
43B VAL* 2.7 61.3 + - + +
45B ILE* 4.5 16.8 - - + -
146B PHE* 4.1 4.3 - - + -
350B LEU* 3.3 20.4 - - + -
352B PHE* 4.1 31.6 - - + -
354B LYS 4.7 0.7 - - - +
355B ILE* 3.6 52.7 - - + +
358B GLY* 5.4 0.2 - - - -
370B THR* 4.7 3.4 - - + -
371B VAL* 1.3 73.8 - - - +
373B THR* 1.3 61.0 + - - +
374B PHE* 4.0 2.2 - - + -
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Residues in contact with THR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL 3.8 10.3 - - - +
42B ALA* 4.6 1.1 - - + -
167B GLU* 4.5 19.5 - - + -
349B VAL* 3.4 25.4 - - + +
350B LEU 2.8 18.8 + - - -
351B PRO* 3.8 5.4 - - - +
352B PHE* 2.9 28.2 + - - +
371B VAL* 4.5 7.9 - - + -
372B LEU* 1.3 75.1 - - - +
374B PHE* 1.3 68.5 + - - +
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Residues in contact with PHE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 6.2 3.6 - - - -
40B MET* 3.1 38.4 - - + +
41B VAL* 3.2 24.3 + - - +
43B VAL* 3.7 30.7 - - + -
145B THR 4.4 1.8 - - - -
147B SER 4.0 5.8 - - - -
148B GLN* 3.8 37.2 - - + -
352B PHE* 3.4 45.3 - + + -
372B LEU* 4.0 8.7 - - + -
373B THR* 1.3 83.1 - - - +
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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