Contacts of the strand formed by residues 193 - 199 (chain A) 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 SER 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.5 13.0 - - - +
190A THR* 2.4 45.5 + - - -
191A PRO 3.2 1.2 + - - -
192A GLY* 1.3 78.4 - - - +
194A THR* 1.3 62.6 + - - +
195A CYS* 4.0 2.0 - - - -
216A ALA* 3.5 3.0 - - - -
217A ALA 2.7 28.2 + - - +
218A ARG 3.1 7.8 + - - +
263A ASP* 3.4 16.4 - - - -
264A PHE* 3.8 13.6 - - - -
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Residues in contact with THR 194 (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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192A GLY 4.9 1.0 + - - -
193A SER* 1.3 75.5 - - - +
195A CYS* 1.3 58.6 + - - +
217A ALA* 5.3 1.2 - - - +
218A ARG* 3.6 23.5 + - + +
220A ILE* 4.4 7.4 - - + -
258A THR* 3.5 34.5 - - + +
261A GLY 4.9 0.7 - - - +
262A VAL* 3.6 19.9 - - + +
263A ASP* 2.8 39.2 + - - +
264A PHE 3.2 5.9 + - - -
101B ARG* 5.1 4.0 - - - +
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Residues in contact with CYS 195 (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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189A VAL* 3.6 42.6 - - - -
193A SER* 4.0 4.0 - - - -
194A THR* 1.3 77.6 - - - +
196A ALA* 1.3 59.7 + - - +
197A VAL* 5.4 0.2 - - + -
211A CYS* 3.8 21.8 - - + -
216A ALA* 3.8 14.4 - - - -
218A ARG 3.0 11.1 + - - +
219A ILE* 3.3 6.7 - - + -
220A ILE* 2.9 26.2 + - - +
262A VAL* 4.5 2.5 - - - -
264A PHE* 3.1 15.7 - - - +
266A PHE* 4.2 2.7 - - + -
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Residues in contact with ALA 196 (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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195A CYS* 1.3 74.2 - - - +
197A VAL* 1.3 58.4 + - - +
198A PHE* 4.1 10.3 - - + -
220A ILE* 3.3 8.5 - - - +
222A VAL* 5.2 1.3 - - + -
254A LEU* 4.5 11.9 - - + -
262A VAL* 3.9 20.5 - - + +
264A PHE 2.9 6.7 + - - -
265A SER* 4.1 3.4 - - - -
266A PHE* 2.9 31.6 + - - -
281A CYS* 4.0 20.0 - - - -
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Residues in contact with VAL 197 (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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196A ALA* 1.3 76.0 - - - +
198A PHE* 1.3 65.5 + - - +
199A GLY 3.9 14.1 + - - +
200A LEU* 4.4 2.9 - - + +
204A GLY* 3.7 22.9 - - - +
207A ALA* 4.1 9.2 - - + -
208A VAL* 4.1 33.7 - - + +
211A CYS* 4.4 7.4 - - - -
219A ILE* 4.6 6.5 - - + -
220A ILE 3.0 8.9 + - - +
221A ALA* 3.6 2.3 - - - -
222A VAL* 2.8 27.9 + - - +
266A PHE* 3.6 18.8 - - + -
268A VAL* 4.4 5.2 - - + -
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Residues in contact with PHE 198 (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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196A ALA* 4.1 12.3 - - + -
197A VAL* 1.3 76.3 - - - +
199A GLY* 1.3 59.0 + - - +
222A VAL* 3.9 26.2 - - + -
243A PRO* 5.8 0.2 - - + -
250A ILE* 4.4 12.6 - - + -
254A LEU* 4.0 20.0 - - + -
265A SER* 4.8 0.2 - - - -
266A PHE 2.8 20.3 + - - +
267A GLU* 4.1 7.6 - - + -
268A VAL* 2.8 30.5 + - - +
269A ILE* 3.6 13.3 - - + +
274A THR* 4.2 21.5 - - + -
277A ALA* 4.2 24.0 - - + -
278A SER* 3.9 24.0 - - - -
281A CYS* 3.8 24.0 - - + -
377A NAD 5.3 0.7 - + - -
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Residues in contact with GLY 199 (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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197A VAL* 3.9 1.6 + - - +
198A PHE* 1.3 72.8 - - - +
200A LEU* 1.3 67.1 + - - +
201A GLY 3.6 2.7 - - - -
204A GLY* 3.0 23.7 - - - -
222A VAL 3.0 12.7 + - - -
223A ASP* 3.8 3.8 - - - -
268A VAL 4.0 3.5 - - - +
269A ILE* 3.6 12.6 - - - +
377A NAD 3.5 21.0 + - - -
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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