Contacts of the strand formed by residues 294 - 298 (chain A) in PDB entry 1KIT
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 ARG 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ASP 3.0 1.2 + - - +
293A PRO* 1.3 70.7 - - - +
295A PRO* 1.3 62.4 - - - +
296A ILE* 5.0 2.9 - - - +
305A LEU 3.8 1.4 - - - +
306A VAL* 3.7 0.4 - - - +
307A SER* 2.6 41.0 + - - +
546A PRO* 3.4 21.7 + - + -
547A GLY* 3.3 35.8 - - - +
548A PRO* 3.7 1.8 - - - +
549A GLY* 3.0 31.0 + - - +
550A HIS 2.9 26.4 + - - -
551A GLY* 3.7 2.9 - - - +
570A TYR* 3.6 27.7 - - + +
571A PRO* 3.6 12.0 + - - +
620A ALA 3.1 20.4 + - - -
621A ASP* 2.8 31.5 + - - +
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Residues in contact with PRO 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A SER* 3.5 12.3 - - - +
228A ILE 5.0 2.0 - - - +
229A VAL* 4.2 11.2 - - + +
239A THR 5.3 0.2 - - - +
241A PHE* 3.5 30.5 - - + -
293A PRO 3.0 14.8 - - - +
294A ARG* 1.3 89.7 - - - +
296A ILE* 1.3 63.9 + - - +
304A VAL* 5.1 4.9 - - + -
305A LEU 3.0 11.4 - - - +
306A VAL* 3.5 17.3 - - + -
549A GLY 3.8 3.4 - - - +
550A HIS* 3.4 11.7 - - + +
551A GLY 2.8 22.2 + - - +
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 4.9 1.6 - - - -
294A ARG 5.0 3.4 - - - +
295A PRO* 1.3 76.0 - - - +
297A TYR* 1.3 64.9 + - - +
298A ASP* 3.7 0.7 + - - +
303A THR 3.5 0.9 - - - +
304A VAL* 3.3 3.9 - - - -
305A LEU* 2.7 49.6 + - + +
307A SER* 6.1 0.2 - - - +
551A GLY* 3.2 29.6 - - - +
552A ILE* 3.0 31.2 - - - +
553A THR* 3.7 5.8 - - - +
568A LEU* 3.4 28.5 - - + -
569A ILE 3.8 22.7 - - - +
570A TYR* 3.9 23.8 - - + -
594A TRP* 4.9 5.2 - - + -
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Residues in contact with TYR 297 (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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229A VAL* 3.0 31.1 - - + +
230A ALA 3.6 14.1 - - - -
231A SER* 3.1 22.1 + - - -
232A SER* 3.3 23.6 - - - -
233A VAL* 3.4 19.4 + - - +
296A ILE* 1.3 75.0 - - - +
298A ASP* 1.3 62.2 + - - +
299A PRO* 3.0 30.0 - - + +
302A ASN* 2.5 31.6 + - - -
303A THR 3.4 20.6 - - - -
304A VAL* 4.5 7.4 - - + +
337A VAL* 4.8 2.9 - - + -
551A GLY 4.8 1.2 + - - -
553A THR* 3.0 20.1 + - - -
744A TYR* 3.9 13.7 + - - +
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE 3.7 2.0 + - - +
297A TYR* 1.3 71.7 - - - +
299A PRO* 1.3 59.4 - - - +
300A SER* 3.7 17.0 + - - -
301A SER* 2.4 28.8 + - - +
302A ASN* 2.6 35.8 + - - -
303A THR* 2.6 19.2 + - - +
305A LEU* 5.9 3.1 - - + -
553A THR* 4.3 11.0 - - - +
566A GLY* 5.4 1.6 - - - +
568A LEU* 4.3 24.1 - - + +
590A GLY* 5.0 6.2 - - - +
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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