Contacts of the strand formed by residues 29 - 35 (chain 1) in PDB entry 3J7Y
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 CYS 29 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191 ARG* 3.7 13.9 - - - -
201 MET 3.4 6.5 - - - +
211 VAL* 3.9 31.6 - - - -
271 GLY* 3.5 8.0 + - - -
281 PHE* 1.3 87.0 - - - +
301 PHE* 1.3 63.4 + - - +
311 ASN* 5.0 0.5 - - - +
2904A A 6.0 0.7 - - - -
2905A A 3.9 23.1 - - + -
2906A C 3.0 45.5 + - + +
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Residues in contact with PHE 30 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 VAL 3.8 0.2 - - - +
191 ARG* 3.5 0.7 - - - -
201 MET* 2.9 58.7 + - + +
281 PHE* 5.2 8.3 - - + -
291 CYS* 1.3 75.2 - - - +
311 ASN* 1.3 68.5 + - - +
321 THR* 3.2 29.6 - - + -
431 LEU* 4.4 4.5 - - + -
451 HIS* 3.1 47.8 - + + +
561 PHE* 4.7 8.2 - + + -
2852A C 3.3 27.6 - + - -
2855A G 4.8 7.2 - - - -
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Residues in contact with ASN 31 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 LEU* 3.9 16.6 - - + -
181 VAL 3.4 4.7 - - - +
191 ARG* 4.3 12.1 + - - +
291 CYS 4.9 0.5 - - - +
301 PHE* 1.3 82.8 + - - +
321 THR* 1.3 67.9 + - - +
621 ILE* 4.5 6.8 - - - +
1343 TRP* 4.9 10.8 - - + +
2851A A 5.6 0.3 + - - -
2906A C 4.6 7.4 - - - +
2907A U 2.6 52.5 + - - +
2908A U 3.7 11.5 + - - -
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Residues in contact with THR 32 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 LEU* 3.5 10.1 - - - +
181 VAL* 2.8 46.4 + - - +
201 MET* 4.0 8.5 - - + +
301 PHE* 3.2 40.8 - - + -
311 ASN* 1.3 80.8 - - - +
331 LYS* 1.3 67.7 + - - +
411 LEU* 4.2 5.5 - - - +
2851A A 4.1 7.0 - - - +
2852A C 3.7 24.8 - - + -
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Residues in contact with LYS 33 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ASN* 3.8 23.7 - - - +
161 ILE 3.4 9.9 - - - +
171 LEU* 5.4 4.0 - - + -
321 THR* 1.3 85.1 + - - +
341 ARG* 1.3 67.4 + - - +
411 LEU* 3.9 0.2 - - - +
651 LEU* 3.5 32.2 - - - +
1343 TRP* 4.1 24.2 - - + -
2848A A 4.5 24.4 + - - -
2849A G 5.6 0.4 + - - -
2850A U 6.0 0.4 - - - +
2851A A 4.3 16.2 - - - +
2852A C 3.6 17.8 + - - -
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Residues in contact with ARG 34 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ASN* 3.4 8.9 + - - -
161 ILE* 2.8 46.9 + - - +
181 VAL* 3.9 15.3 - - + +
331 LYS* 1.3 79.5 - - - +
351 ASN* 1.3 84.2 + - - +
361 ARG* 4.5 8.1 + - - +
381 ARG* 2.8 32.3 + - + +
391 GLU 3.3 23.1 + - - +
401 LYS* 3.6 9.5 - - - +
411 LEU* 3.9 22.1 - - + +
581 GLU* 2.8 38.2 + - - +
2852A C 5.7 0.2 - - - +
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Residues in contact with ASN 35 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141 LYS* 3.5 28.4 + - - +
151 ASN* 3.0 25.9 + - - +
341 ARG* 1.3 91.1 + - - +
361 ARG* 1.3 65.0 + - - +
371 LEU* 3.2 14.1 + - + +
381 ARG* 3.2 30.4 - - + +
2849A G 4.2 8.4 + - - -
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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