Contacts of the helix formed by residues 298 - 307 (chain A) in PDB entry 5SY1
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 LEU 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A TYR* 6.4 0.9 - - + -
294A ILE* 3.5 33.0 + - + +
297A VAL* 1.3 80.0 - - + +
299A PRO* 1.3 65.9 - - + +
301A LEU* 3.8 17.3 - - + -
302A HIS* 3.0 42.6 + - + +
342A GLU* 3.8 38.1 - - + +
345A TYR* 5.3 6.7 - - + -
346A VAL* 4.6 18.6 - - + -
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Residues in contact with PRO 299 (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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177A ILE 4.8 8.5 - - - +
178A TYR* 3.9 30.5 - - + -
294A ILE 4.2 5.4 - - - +
295A SER* 4.3 9.4 - - - +
296A GLY* 4.1 5.4 - - - +
297A VAL 3.6 11.2 - - - +
298A LEU* 1.3 92.3 - - + +
300A THR* 1.3 63.3 + - + +
301A LEU 3.2 3.6 + - - -
302A HIS* 3.9 3.2 + - + +
303A ILE* 3.3 32.7 + - + +
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Residues in contact with THR 300 (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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296A GLY 4.3 9.3 + - - +
297A VAL* 3.0 19.5 + - - +
299A PRO* 1.3 81.0 - - + +
301A LEU* 1.3 64.7 + - - +
303A ILE* 4.6 10.8 - - + -
304A VAL* 3.8 18.0 - - - +
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Residues in contact with LEU 301 (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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297A VAL* 3.4 27.6 - - + +
298A LEU* 3.2 31.2 + - + +
299A PRO 3.1 1.0 - - - -
300A THR* 1.3 85.5 - - - +
302A HIS* 1.3 63.9 + - + +
303A ILE 3.2 1.6 - - - -
304A VAL* 3.4 7.6 + - + +
305A ARG* 3.0 26.7 + - - +
338A LEU* 5.6 9.3 - - + +
341A VAL* 5.0 17.5 - - + +
342A GLU* 4.6 24.5 - - + +
345A TYR* 5.5 4.7 - - + -
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Residues in contact with HIS 302 (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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298A LEU* 3.0 40.4 + - + +
299A PRO* 4.7 2.9 - - + +
301A LEU* 1.3 73.3 - - - +
303A ILE* 1.3 56.7 + - + +
305A ARG* 3.1 8.9 + - - +
306A ARG* 2.7 52.9 + - + +
342A GLU* 3.1 35.6 + - - -
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Residues in contact with ILE 303 (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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299A PRO* 3.3 24.4 + - + +
300A THR* 4.8 9.2 - - + -
301A LEU 3.2 0.6 - - - -
302A HIS* 1.3 77.3 - - + +
304A VAL* 1.3 57.5 + - + +
306A ARG* 3.9 4.4 - - - +
307A GLY* 2.6 33.7 + - - +
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Residues in contact with VAL 304 (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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300A THR 3.8 17.7 - - - +
301A LEU* 3.4 10.4 + - + +
302A HIS 3.3 0.4 - - - -
303A ILE* 1.3 78.4 - - + +
305A ARG* 1.3 64.3 - - - +
306A ARG 3.3 0.7 + - - -
307A GLY 3.6 21.6 - - - +
308A VAL* 3.6 10.0 - - - +
338A LEU* 4.0 23.0 - - + +
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Residues in contact with ARG 305 (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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301A LEU 3.0 17.5 + - - +
302A HIS* 3.1 13.7 + - - +
304A VAL* 1.3 76.0 - - - +
306A ARG* 1.3 62.7 + - + +
308A VAL* 3.4 14.0 - - - +
335A VAL* 5.2 7.2 - - + +
338A LEU* 5.1 17.0 - - + +
342A GLU* 5.8 4.3 - - - +
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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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302A HIS* 2.7 34.8 + - + +
303A ILE* 3.9 4.5 - - - +
305A ARG* 1.3 75.2 - - + +
307A GLY* 1.3 60.3 + - - +
308A VAL* 2.8 17.0 + - - +
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Residues in contact with GLY 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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303A ILE* 2.6 22.4 + - - +
304A VAL* 3.6 12.4 - - - +
306A ARG* 1.3 68.8 - - - +
308A VAL* 1.3 63.3 + - - +
309A ASP* 3.5 6.6 + - - +
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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