Contacts of the strand formed by residues 285 - 290 (chain C) in PDB entry 1SID
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 ILE 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B LEU* 4.5 11.0 - - + -
57C MET* 4.7 11.9 - - + -
96C PRO* 4.7 9.4 - - + -
160C SER 3.4 13.2 - - - +
161C GLN* 3.0 8.4 - - - +
162C TYR* 2.5 65.0 + - + +
163C HIS* 3.2 7.8 - - - -
224C VAL* 4.9 9.4 - - + -
283C VAL* 4.3 6.5 - - + -
284C ASP* 1.3 79.3 - - - +
286C MET* 1.3 63.0 + - - +
287C GLY 3.4 7.4 - - - +
299C TRP* 3.3 38.8 - - + +
300C ARG 3.9 3.8 - - - -
301C GLY* 4.5 1.1 - - - -
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Residues in contact with MET 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C VAL* 5.5 0.4 - - - -
135C LEU* 5.2 14.1 - - + -
157C VAL* 4.1 8.5 - - + +
159C GLY 4.3 0.7 - - - +
161C GLN* 3.3 32.5 + - - +
163C HIS* 3.2 31.6 - - + +
251C PRO* 3.8 31.8 - - + +
253C LEU* 3.5 27.6 - - + -
284C ASP 3.6 12.3 - - - +
285C ILE* 1.3 75.4 - - - +
287C GLY* 1.3 58.1 + - - +
300C ARG* 2.8 20.1 + - + +
301C GLY* 4.1 5.2 - - - -
302C LEU* 3.7 29.2 - - + -
243D TYR* 5.9 0.9 - - - -
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Residues in contact with GLY 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C VAL* 3.3 12.4 - - - +
158C GLU 3.3 11.7 - - - -
159C GLY 4.3 0.4 - - - -
160C SER 3.3 18.6 - - - -
285C ILE* 3.4 6.3 - - - +
286C MET* 1.3 80.5 - - - +
288C TRP* 1.3 57.4 + - - -
299C TRP* 2.8 19.9 - - - +
300C ARG 2.9 12.1 + - - +
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Residues in contact with TRP 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU 5.8 0.4 - - - -
136B LEU* 4.7 6.1 - - + -
138B VAL* 4.0 32.1 - - + -
153B ILE* 5.1 8.0 - - + +
156B PRO* 5.5 2.7 - - + -
79C ILE* 5.5 1.6 - - + -
156C PRO 4.2 1.9 - - - +
157C VAL* 3.3 16.3 - - - +
158C GLU 2.8 26.2 + - - +
159C GLY* 3.3 14.7 - - - -
160C SER* 3.5 36.8 - - - -
246C GLY 4.0 6.2 + - - -
247C THR* 3.8 11.3 + - - +
287C GLY* 1.3 72.9 - - - -
289C ARG* 1.3 61.7 + - - +
290C VAL* 3.9 6.0 + - + +
297C HIS* 3.4 47.2 - + + -
299C TRP* 2.9 70.9 - + + +
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Residues in contact with ARG 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLN 5.8 1.0 + - - -
72C TYR* 4.5 14.3 - - - -
75C TRP* 3.7 40.8 - - + +
141C PHE 4.2 10.9 + - - -
142C ASN* 3.0 26.9 - - - +
156C PRO 5.2 1.6 - - - -
157C VAL* 4.3 12.8 - - + +
287C GLY 4.0 1.4 + - - -
288C TRP* 1.3 73.5 - - - +
290C VAL* 1.3 57.0 + - - +
291C THR* 3.6 24.9 - - - +
296C VAL 3.9 0.9 - - - +
297C HIS* 3.2 1.7 - - - -
298C HIS* 2.7 67.1 + - - +
300C ARG 4.8 0.4 - - - +
85D ASP* 3.8 20.8 + - - -
180D ASP* 5.3 7.5 + - - -
182D ARG* 5.8 2.2 - - - +
3I SIA 4.4 3.2 + - - -
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Residues in contact with VAL 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ASN* 3.4 13.2 + - - +
143C LYS* 3.2 35.0 + - + -
155C THR* 5.0 17.1 + - + +
156C PRO 5.1 2.4 + - - +
288C TRP* 4.3 8.5 - - + +
289C ARG* 1.3 73.9 - - - +
291C THR* 1.3 73.0 + - - +
292C ARG 3.3 0.2 + - - -
295C ASP* 4.3 11.7 - - - +
296C VAL 3.7 4.0 - - - +
297C HIS* 4.0 42.4 - - + +
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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