Contacts of the strand formed by residues 299 - 304 (chain B) in PDB entry 4HYY
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 THR 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 3.9 27.8 - - + -
117B GLU* 6.1 0.7 - - - +
121B ILE 3.2 2.3 + - - +
122B THR* 3.3 15.1 - - + -
123B GLU* 2.6 35.2 + - - +
297B SER* 4.1 0.5 - - - -
298B THR* 1.3 90.4 + - - +
300B ARG* 1.3 61.2 + - - +
301B ILE* 4.0 13.2 - - + -
315B ILE* 4.9 10.3 - - + -
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Residues in contact with ARG 300 (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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123B GLU* 2.8 52.8 + - - -
125B PHE* 3.4 17.0 - - + -
268B ASN* 4.8 0.6 + - - -
287B PRO* 3.5 22.3 - - - +
288B ILE 4.9 3.8 + - - -
290B GLY* 4.4 4.4 + - - -
293B LEU* 5.1 2.0 - - - +
294B ALA* 3.1 45.1 + - - +
297B SER* 3.2 18.2 - - - +
298B THR 4.4 1.1 + - - +
299B THR* 1.3 77.0 - - - +
301B ILE* 1.3 64.2 + - - +
315B ILE* 3.4 12.2 - - - +
316B TYR* 2.8 55.8 + - + +
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Residues in contact with ILE 301 (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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108B PHE* 4.2 15.0 - - + -
111B LEU* 5.8 0.7 - - + -
112B LEU* 3.8 23.6 - - + -
116B ILE* 5.5 0.7 - - + -
122B THR* 3.6 31.0 - - + -
123B GLU 2.7 14.0 + - - +
124B ALA* 3.3 9.2 - - + -
125B PHE* 2.9 32.2 + - - +
265B PHE* 5.4 2.9 - - + -
299B THR* 4.0 7.6 - - + -
300B ARG* 1.3 78.9 - - - +
302B SER* 1.3 74.8 + - - +
303B LEU* 3.8 17.3 - - + -
313B ALA* 3.9 14.6 - - + -
314B LYS 3.4 6.7 - - - +
315B ILE* 5.0 6.5 - - + -
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Residues in contact with SER 302 (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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125B PHE* 3.4 27.1 - - - -
270B MET* 6.4 0.9 - - - -
300B ARG 4.3 0.2 + - - -
301B ILE* 1.3 75.0 - - - +
303B LEU* 1.3 65.9 + - - +
304B ARG* 4.9 8.7 - - - -
312B ILE 3.4 1.5 + - - +
313B ALA* 3.2 8.0 - - - -
314B LYS* 2.7 45.4 + - - +
316B TYR* 4.4 9.7 - - - +
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Residues in contact with LEU 303 (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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108B PHE* 4.7 5.4 - - + -
124B ALA* 4.3 11.7 - - + -
125B PHE 2.8 15.4 + - - +
126B GLY* 3.5 9.6 - - - -
127B GLU 4.4 0.9 + - - -
130B THR* 3.0 31.8 + - + -
131B GLY* 3.9 5.6 - - - +
132B LYS* 3.7 39.9 - - + +
135B LEU* 5.3 4.7 - - + -
270B MET* 5.6 1.7 - - - +
301B ILE* 3.8 17.0 - - + -
302B SER* 1.3 85.3 - - - +
304B ARG* 1.3 63.2 + - - +
312B ILE 3.3 3.4 - - - +
313B ALA* 4.0 14.1 - - + -
328B PHE* 4.3 17.9 - - + -
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Residues in contact with ARG 304 (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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130B THR* 4.4 4.7 - - - -
302B SER* 4.9 10.1 - - - +
303B LEU* 1.3 76.3 - - - +
305B LYS* 1.3 71.2 + - - +
311B ARG* 3.5 9.6 - - - +
312B ILE* 2.9 65.7 + - + +
314B LYS* 6.2 2.2 - - - -
325B GLU* 4.8 7.9 + - - -
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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