Contacts of the strand formed by residues 305 - 312 (chain A) in PDB entry 2A1H
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 VAL 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A VAL* 4.5 2.2 - - + -
246A TYR 4.1 6.7 - - - +
247A TRP* 3.9 9.9 - - + -
296A LEU* 4.0 13.0 - - + -
299A ALA* 3.7 28.4 + - + -
300A LEU* 3.9 26.7 - - + +
303A GLY* 3.5 5.8 - - - +
304A ARG* 1.3 77.2 - - - +
306A ARG* 1.3 64.8 - - - +
307A GLU 4.1 4.3 - - - +
308A VAL* 3.9 27.8 - - + -
332A ILE* 4.2 12.8 - - + -
333A PRO* 3.4 21.5 - - + +
337A ASN* 3.9 2.1 + - - -
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Residues in contact with ARG 306 (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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246A TYR* 2.9 53.7 + - + +
247A TRP* 5.0 0.7 - - - -
248A THR* 5.4 2.7 - - - +
254A LEU* 3.8 34.1 - - - +
304A ARG 3.7 7.2 + - - +
305A VAL* 1.3 76.8 - - - +
307A GLU* 1.3 68.4 + - + +
333A PRO 3.5 1.0 - - - +
334A THR* 3.5 12.5 + - - -
337A ASN* 3.0 39.9 + - + +
340A GLU* 3.1 35.0 + - - +
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Residues in contact with GLU 307 (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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244A PHE 4.2 0.2 - - - +
246A TYR* 2.7 54.0 + - + +
305A VAL* 4.0 1.3 - - - +
306A ARG* 1.3 88.3 + - - +
308A VAL* 1.3 66.7 + - - +
309A PHE* 4.5 5.5 - - + -
334A THR* 3.7 26.9 - - + +
337A ASN* 4.1 5.2 - - + +
339A PRO* 3.5 4.4 - - - +
340A GLU* 3.5 14.6 + - - +
341A LEU* 2.9 30.2 + - - +
342A ILE* 3.0 40.0 + - + +
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Residues in contact with VAL 308 (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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184A LEU* 5.7 0.2 - - + -
235A LEU* 5.9 0.9 - - + -
243A ILE* 4.1 22.7 - - + -
244A PHE 3.4 11.0 - - - +
245A VAL* 4.0 18.4 - - + -
296A LEU* 4.6 8.7 - - + -
305A VAL* 3.9 11.9 - - + -
307A GLU* 1.3 78.8 - - - +
309A PHE* 1.3 67.0 + - - +
319A PRO* 3.8 1.6 - - - +
320A VAL* 3.0 43.3 + - + -
323A ILE* 5.2 6.3 - - + -
332A ILE* 3.6 26.2 - - + -
334A THR* 3.1 11.9 + - - +
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Residues in contact with PHE 309 (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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238A VAL* 5.0 0.4 - - - -
243A ILE* 3.6 6.1 - - - +
244A PHE* 2.8 64.9 + + + +
246A TYR* 4.8 2.7 - - + -
256A LEU* 3.9 10.5 - - + -
274A LEU* 3.7 16.2 - - + -
307A GLU* 4.5 6.7 - - + -
308A VAL* 1.3 82.5 - - - +
310A GLY* 1.3 63.4 + - - +
317A VAL* 3.7 29.6 - - + -
318A CYS 3.2 20.6 - - - +
320A VAL* 4.3 6.5 - - - -
341A LEU* 4.2 14.4 - - + -
342A ILE* 3.7 28.0 - - + -
345A PHE* 3.7 24.5 - + - -
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Residues in contact with GLY 310 (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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238A VAL* 4.4 11.9 - - - -
241A MET* 4.0 20.1 - - - +
242A ASN 3.1 9.2 - - - -
309A PHE* 1.3 76.0 - - - +
311A SER* 1.3 60.1 + - - -
317A VAL* 3.5 4.3 - - - -
318A CYS* 2.8 36.5 + - - +
320A VAL* 4.7 2.4 - - - +
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Residues in contact with SER 311 (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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241A MET* 3.3 10.7 - - - +
242A ASN* 2.8 43.8 + - - +
244A PHE* 3.4 20.3 - - - -
270A VAL* 4.0 5.8 - - - -
271A ARG* 3.8 10.2 + - - -
274A LEU* 3.9 22.9 - - - -
309A PHE* 5.2 0.2 - - - -
310A GLY* 1.3 74.0 - - - -
312A GLY* 1.3 58.9 + - - +
316A GLN 3.3 14.4 - - - -
317A VAL* 5.1 0.2 - - - -
400A PLP 4.0 3.5 - - - +
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Residues in contact with GLY 312 (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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241A MET* 4.4 4.2 - - - +
270A VAL* 3.6 9.8 - - - +
311A SER* 1.3 76.5 - - - +
313A THR* 1.3 60.7 + - - -
314A ALA 3.4 2.5 - - - -
315A CYS 4.2 0.9 - - - -
316A GLN* 2.8 33.1 + - - +
400A PLP 3.7 16.6 - - - -
502A GBN 3.4 13.7 - - - -
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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