Contacts of the strand formed by residues 271 - 279 (chain K) in PDB entry 1HZH
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 GLU 271 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B GAL 3.4 48.1 + - - +
257K PRO 4.1 0.3 - - - -
258K PRO* 3.4 23.0 - - - +
262K ASP* 5.2 0.2 + - - -
269K THR* 3.7 11.5 - - - +
270K PRO* 1.3 78.0 - - + +
272K VAL* 1.3 62.9 + - - +
273K THR* 4.2 2.4 + - - -
307K LYS* 5.7 0.9 + - - -
324K VAL* 3.1 35.5 - - + +
325K LEU 3.3 13.7 - - - +
326K THR* 3.8 12.1 - - + +
327K VAL* 4.2 2.0 - - - +
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Residues in contact with VAL 272 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255K LEU* 4.7 1.8 - - + -
256K PHE 3.3 8.3 - - - +
258K PRO* 4.1 7.2 - - + -
271K GLU* 1.3 76.1 - - - +
273K THR* 1.3 60.6 + - - +
290K TRP* 3.7 26.2 - - + -
324K VAL* 4.0 0.5 - - - -
325K LEU* 3.0 41.2 + - + +
327K VAL* 3.9 19.3 - - + +
332K TRP* 4.1 17.7 - - + -
338K TYR* 4.1 11.4 - - + -
355K ILE* 3.9 23.3 - - + -
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Residues in contact with THR 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B NAG 3.5 29.0 - - - +
6B GAL 3.2 22.7 + - - -
254K PHE 3.4 2.6 - - - +
255K LEU* 3.3 6.3 - - - -
256K PHE* 2.7 43.5 + - - -
271K GLU* 3.9 9.0 + - - -
272K VAL* 1.3 73.8 + - - +
274K CYS* 1.3 61.4 + - - +
275K VAL* 3.8 6.3 - - + -
307K LYS* 5.9 0.7 - - - +
322K VAL* 3.4 29.4 - - + -
323K SER 3.7 4.3 - - - +
324K VAL* 4.4 6.0 - - + +
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Residues in contact with CYS 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253K VAL* 3.5 25.4 - - - -
254K PHE 3.7 2.2 - - - -
255K LEU* 3.9 3.8 - - + -
273K THR* 1.3 70.3 - - - +
275K VAL* 1.3 61.4 + - - +
276K VAL 4.1 0.2 + - - -
288K PHE* 4.3 3.5 - - - -
290K TRP* 3.3 18.5 - - + -
321K VAL 3.8 1.0 - - - +
322K VAL* 3.5 2.8 - - - +
323K SER* 2.9 41.4 + - - +
340K CYS* 2.0 50.0 - - + -
342K VAL* 4.0 7.0 - - - -
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Residues in contact with VAL 275 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B NAG 3.8 9.2 - - - +
5B NAG 4.4 2.0 - - - -
252K SER 3.4 1.7 - - - +
253K VAL* 3.4 3.4 - - - -
254K PHE* 2.9 45.6 + - + +
256K PHE* 4.2 17.5 - - + -
273K THR* 3.8 14.8 - - + -
274K CYS* 1.3 77.1 - - - +
276K VAL* 1.3 64.2 + - - +
277K VAL* 3.9 10.0 + - + -
320K ARG* 3.6 40.2 - - + +
321K VAL 3.7 2.2 - - - -
322K VAL* 3.5 23.8 - - + -
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Residues in contact with VAL 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K PRO* 3.9 22.2 - - + -
252K SER 3.3 10.1 - - - +
253K VAL* 4.3 2.7 - - + -
274K CYS 5.1 0.2 - - - -
275K VAL* 1.3 75.1 - - - +
277K VAL* 1.3 63.3 + - - +
279K VAL* 3.9 14.3 - - + +
286K VAL* 4.4 4.9 - - + -
288K PHE* 3.4 40.4 - - + -
319K TYR 3.9 0.9 - - - +
320K ARG* 3.3 6.2 - - - +
321K VAL* 2.8 38.6 + - + +
342K VAL* 3.7 30.7 - - + -
344K ASN* 6.5 0.2 - - + -
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Residues in contact with VAL 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 3.6 17.9 - - - +
2B NAG 3.1 40.4 - - - +
251K PRO* 3.3 2.8 - - - +
252K SER* 2.9 48.0 + - - +
254K PHE* 3.9 14.6 - - + -
275K VAL* 3.9 10.1 - - + -
276K VAL* 1.3 78.1 - - - +
278K ASP* 1.3 81.1 - - - +
279K VAL* 3.4 2.8 - - - +
312K GLN* 6.4 0.7 - - + -
319K TYR 3.7 4.5 - - - -
320K ARG* 4.5 6.5 - - + +
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Residues in contact with ASP 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 3.0 49.3 + - - +
2B NAG 5.2 1.2 + - - -
250K GLY* 3.6 18.1 - - - +
251K PRO* 3.3 18.5 - - - +
252K SER* 5.3 2.6 + - - -
277K VAL* 1.3 84.4 - - + +
279K VAL* 1.3 60.2 + - - +
280K SER 3.8 2.9 + - - -
312K GLN* 5.8 0.8 - - - +
318K THR* 3.4 28.1 + - + +
319K TYR 3.3 5.7 + - - -
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Residues in contact with VAL 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K PRO* 4.8 7.2 - - + -
276K VAL* 3.9 27.6 - - + +
278K ASP* 1.3 75.7 - - - +
280K SER* 1.3 64.6 + - - +
281K HIS 3.7 0.5 + - - -
283K ASP 3.7 5.8 - - - +
284K PRO* 3.6 36.3 - - + +
286K VAL* 3.9 9.6 - - + -
318K THR* 3.8 1.6 - - - -
319K TYR* 2.8 53.3 + - + +
321K VAL* 3.8 18.4 - - + -
344K ASN* 4.8 4.3 - - - +
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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