Contacts of the strand formed by residues 277 - 285 (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 GLY 277 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C LYS* 3.9 17.2 - - - +
103C LEU 3.4 8.7 - - - -
104C GLN* 3.9 2.2 + - - +
169C GLY 3.6 9.9 - - - +
273C CYS* 2.7 33.1 - - - +
274C LYS 3.5 1.8 + - - -
275C GLY 3.3 3.4 - - - -
276C GLU* 1.3 79.8 - - - +
278C LEU* 1.3 59.9 + - - -
279C TYR* 3.8 7.9 - - - -
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Residues in contact with LEU 278 (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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49C ILE* 4.8 4.0 - - + -
101C ALA 3.8 0.9 - - - +
102C LYS* 3.2 3.8 - - - +
103C LEU* 2.7 57.6 + - + +
105C LEU* 3.7 9.9 - - + -
122C ALA* 5.1 3.4 - - + -
167C VAL* 4.0 24.2 - - + -
168C GLY 3.7 8.7 - - - +
271C PRO* 6.5 0.2 - - + -
273C CYS* 4.2 14.6 - - - -
277C GLY* 1.3 74.8 - - - -
279C TYR* 1.3 76.3 - - - +
280C LEU* 3.9 8.8 + - + -
308C ILE* 4.1 28.3 - - + -
310C LEU* 3.8 23.6 - - + -
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Residues in contact with TYR 279 (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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100C MET* 5.2 11.2 - - + -
101C ALA 3.7 4.9 - - - +
102C LYS* 3.4 43.0 + - + +
166C ALA 3.4 5.4 - - - +
167C VAL* 3.4 0.3 - - - -
168C GLY 2.6 45.6 + - - +
169C GLY 3.5 9.2 - - - -
170C GLU* 3.4 31.4 - - - +
171C PRO* 3.3 41.5 - - + +
172C LEU 5.2 0.2 - - - +
237C THR* 4.6 0.8 - - + +
274C LYS 4.4 4.7 + - - -
277C GLY* 3.8 8.7 - - - -
278C LEU* 1.3 78.3 - - - +
280C LEU* 1.3 64.8 + - - +
281C SER* 3.7 7.0 + - - +
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Residues in contact with LEU 280 (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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51C ALA* 5.1 8.3 - - + -
53C LEU* 4.1 20.6 - - + -
100C MET* 2.9 5.6 - - - +
101C ALA 2.8 36.5 + - - +
103C LEU* 3.7 27.4 - - + -
166C ALA 3.5 3.1 - - - +
167C VAL* 3.8 23.6 - - + -
278C LEU* 4.0 8.3 - - + -
279C TYR* 1.3 77.7 - - - +
281C SER* 1.3 62.6 + - - +
306C PHE* 3.9 32.1 - - + -
308C ILE* 4.0 23.6 - - + -
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Residues in contact with SER 281 (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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53C LEU* 4.6 0.7 - - - -
98C TRP* 4.4 9.2 - - - -
99C SER 3.4 6.5 - - - -
100C MET* 3.7 11.7 - - - +
165C PHE* 3.0 2.6 - - - +
166C ALA* 2.6 52.7 + - - +
172C LEU* 4.1 14.7 + - - +
216C LEU* 3.8 16.8 - - - +
237C THR* 4.9 0.9 - - - +
279C TYR* 3.7 8.8 + - - +
280C LEU* 1.3 78.7 - - - +
282C CYS* 1.3 60.9 + - - +
306C PHE* 4.4 1.3 - - - -
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Residues in contact with CYS 282 (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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53C LEU* 3.9 23.5 - - - +
55C PRO* 6.4 1.3 - - - -
98C TRP* 4.0 6.0 - - - -
99C SER* 2.8 30.0 + - - +
164C VAL 2.9 15.5 - - - +
165C PHE* 3.3 15.0 - - + +
281C SER* 1.3 75.0 - - - +
283C VAL* 1.3 73.7 + - - +
284C ASP* 3.8 9.9 - - - -
304C ARG* 3.8 29.8 - - - +
306C PHE* 3.9 1.3 - - + -
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Residues in contact with VAL 283 (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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55C PRO* 6.2 1.6 - - - -
97C THR 4.2 3.6 - - - +
98C TRP* 3.6 37.5 - - + -
99C SER* 4.0 3.8 - - - +
162C TYR* 3.5 31.9 - - + -
163C HIS* 2.8 27.2 - - - -
164C VAL* 2.7 26.6 + - + +
224C VAL* 3.8 15.7 - - + -
282C CYS* 1.3 83.6 - - - +
284C ASP* 1.3 67.7 + - - +
285C ILE* 4.3 9.0 - - + -
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Residues in contact with ASP 284 (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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55C PRO* 5.2 6.1 - - - +
57C MET* 5.0 3.9 - - - +
129C VAL* 3.5 15.6 - - + +
162C TYR 3.2 3.6 - - - -
163C HIS* 3.0 25.9 + - + +
282C CYS* 3.8 5.4 - - - -
283C VAL* 1.3 83.7 - - - +
285C ILE* 1.3 65.8 + - - +
286C MET* 3.3 3.3 + - - +
301C GLY* 3.0 23.0 - - - -
302C LEU* 3.4 28.4 + - + +
304C ARG* 2.6 45.2 + - - +
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Residues in contact with ILE 285 (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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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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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