Contacts of the strand formed by residues 370 - 376 (chain A) in PDB entry 2I69
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 LYS 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A THR 4.4 1.0 - - - +
148A THR* 3.6 22.4 + - + +
150A GLU* 5.6 3.8 + - - -
312A LEU* 3.8 16.3 - - + +
326A GLU* 3.4 32.5 + - - +
327A LEU 3.4 11.7 - - - +
328A GLN* 4.1 21.8 - - + +
368A ASN 3.6 2.4 + - - +
369A ALA* 1.3 81.6 - - - +
371A VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO* 6.2 1.1 - - + -
147A THR 3.8 8.7 - - - +
309A PHE* 4.5 3.6 - - + -
326A GLU* 3.2 5.4 - - - +
327A LEU* 2.8 48.0 + - + +
338A VAL* 4.4 10.8 - - + -
357A THR* 5.8 0.4 - - + -
360A PRO* 5.0 3.1 - - + -
361A PHE 4.1 16.2 - - - +
362A VAL* 4.2 24.9 - - + -
369A ALA* 5.1 2.2 - - + +
370A LYS* 1.3 78.4 - - - +
372A LEU* 1.3 76.1 + - - +
373A ILE* 3.6 21.1 + - + +
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Residues in contact with LEU 372 (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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4A LEU* 4.2 12.1 - - + -
147A THR* 3.1 27.6 + - + +
148A THR* 4.0 2.4 - - - +
149A VAL* 3.9 37.7 - - + +
152A HIS* 3.9 33.4 - - + +
324A VAL* 3.8 26.5 - - + -
325A LEU 3.6 5.6 - - - +
326A GLU* 4.1 4.0 - - + +
357A THR* 4.2 12.2 - - - +
371A VAL* 1.3 87.0 - - - +
373A ILE* 1.3 77.6 + - - +
374A GLU* 4.1 4.3 - - + +
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Residues in contact with ILE 373 (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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323A VAL 3.6 0.9 - - - +
324A VAL* 3.3 4.2 - - - +
325A LEU* 2.8 47.8 + - + +
327A LEU* 4.5 4.5 - - + -
338A VAL* 4.9 5.4 - - + -
340A ILE* 4.0 34.8 - - + -
355A LEU* 5.1 3.6 - - + -
357A THR* 3.8 9.6 - - + -
360A PRO* 3.6 28.5 - - + -
371A VAL* 3.6 21.5 - - + +
372A LEU* 1.3 86.5 - - - +
374A GLU* 1.3 75.3 + - - +
375A LEU* 4.2 11.4 - - + -
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Residues in contact with GLU 374 (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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4A LEU* 4.4 12.7 - - + +
9A ARG* 2.7 47.7 + - - -
144A HIS* 4.4 7.8 - - - -
152A HIS* 5.9 0.5 + - - -
318A THR* 3.5 8.3 - - - +
322A THR* 2.7 19.9 + - - +
323A VAL 3.1 11.2 - - - +
324A VAL* 4.5 7.6 - - + -
355A LEU* 4.4 0.2 - - - -
356A VAL* 2.8 43.8 + - + +
357A THR* 2.9 24.7 + - - +
372A LEU* 4.8 5.8 - - + -
373A ILE* 1.3 77.2 - - - +
375A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 375 (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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322A THR* 3.4 4.8 - - - -
323A VAL* 2.7 60.4 + - + +
325A LEU* 4.9 2.9 - - + -
340A ILE* 3.8 33.4 - - + -
341A SER 5.1 4.0 - - - +
342A SER* 5.0 9.0 - - - -
354A ARG 3.8 2.5 - - - +
355A LEU* 3.8 23.8 - - + -
356A VAL* 3.7 6.1 - - - +
373A ILE* 4.2 6.3 - - + -
374A GLU* 1.3 76.4 - - - +
376A GLU* 1.3 60.7 + - - +
377A PRO* 3.4 19.2 - - + +
384A ILE* 4.5 22.0 - - + -
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Residues in contact with GLU 376 (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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11A PHE* 5.7 2.8 - - - -
34A MET* 5.3 3.6 - - - +
321A GLY 3.7 15.9 - - - +
322A THR* 3.9 16.4 - - + +
342A SER* 5.3 0.8 - - - -
353A GLY* 3.3 6.1 - - - -
354A ARG* 2.8 63.3 + - + +
356A VAL* 4.1 6.1 - - + +
375A LEU* 1.3 72.6 - - - +
377A PRO* 1.3 70.1 - - - +
378A PRO* 5.5 1.2 - - - +
399A LYS* 4.2 7.4 + - - +
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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