Contacts of the strand formed by residues 277 - 285 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D LYS* 4.0 13.6 - - - +
103D LEU 3.6 5.4 - - - -
104D GLN* 4.9 0.2 - - - -
169D GLY* 3.5 2.1 - - - -
273D CYS* 2.9 24.8 - - - +
274D LYS 3.3 1.7 + - - -
275D GLY* 2.9 8.1 + - - -
276D GLU* 1.3 78.4 - - - +
278D LEU* 1.3 61.4 + - - -
279D TYR* 3.2 30.2 - - - -
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Residues in contact with LEU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 4.8 4.0 - - + -
102D LYS* 3.3 1.3 - - - +
103D LEU* 2.7 62.0 + - + +
105D LEU* 3.9 10.3 - - + -
122D ALA* 5.3 3.1 - - + -
167D VAL* 4.2 16.6 - - + -
168D GLY 3.7 7.6 - - - +
273D CYS* 3.9 13.0 - - - -
276D GLU 3.7 0.4 + - - -
277D GLY* 1.3 74.0 - - - -
279D TYR* 1.3 73.6 + - - +
280D LEU* 3.7 13.1 + - + -
308D ILE* 3.9 19.1 - - + -
310D LEU* 3.3 30.7 - - + -
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Residues in contact with TYR 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D MET* 5.0 10.8 - - + -
101D ALA 3.6 5.6 - - - +
102D LYS* 3.3 39.3 + - + +
166D ALA 3.5 5.0 - - - +
167D VAL* 3.5 2.3 - - - -
168D GLY* 2.8 39.8 + - - +
169D GLY 3.7 2.5 - - - -
170D GLU* 3.3 36.6 - - - +
171D PRO* 3.2 36.9 - - + +
172D LEU 5.2 0.7 - - - +
237D THR* 5.8 0.4 - - + -
274D LYS 4.2 7.4 + - - -
275D GLY* 5.7 0.7 - - - -
277D GLY* 3.2 30.6 - - - -
278D LEU* 1.3 71.8 - - - +
280D LEU* 1.3 62.2 + - - +
281D SER* 4.0 6.4 + - - +
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ALA* 5.1 7.0 - - + -
53D LEU* 4.2 18.2 - - + -
100D MET* 3.1 5.4 - - - +
101D ALA 2.9 35.3 + - - +
103D LEU* 3.8 24.9 - - + -
166D ALA 3.9 7.0 - - - +
167D VAL* 4.0 18.6 - - + -
278D LEU* 4.1 7.2 - - + -
279D TYR* 1.3 78.8 - - - +
281D SER* 1.3 63.5 + - - +
306D PHE* 3.5 39.7 - - + -
308D ILE* 3.8 25.1 - - + -
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 4.2 1.9 - - - +
98D TRP* 4.2 7.9 - - - -
99D SER 3.4 7.4 - - - -
100D MET* 4.0 0.6 - - - +
165D PHE* 3.0 1.7 - - - +
166D ALA* 2.7 45.7 + - - +
172D LEU* 4.2 15.8 + - - +
216D LEU* 3.9 25.6 - - - +
237D THR* 5.2 1.2 - - - +
279D TYR* 4.0 8.3 + - - +
280D LEU* 1.3 80.8 + - - +
282D CYS* 1.3 65.7 + - - +
306D PHE* 4.6 2.5 - - - -
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Residues in contact with CYS 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.4 32.1 - - - -
98D TRP* 3.5 10.4 - - - -
99D SER* 2.9 36.9 + - - +
164D VAL 3.0 18.4 - - - +
165D PHE* 3.3 10.1 - - + -
281D SER* 1.3 76.9 - - - +
283D VAL* 1.3 68.1 + - - +
284D ASP* 4.0 7.9 - - - -
304D ARG* 3.9 23.6 - - - +
306D PHE* 4.2 0.4 - - + -
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Residues in contact with VAL 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D PRO* 6.5 0.4 - - - -
97D THR 4.0 6.1 - - - +
98D TRP* 3.7 19.1 - - + -
99D SER* 4.1 6.1 - - - +
162D TYR* 3.3 36.1 - - + -
163D HIS* 3.0 10.9 - - - -
164D VAL* 3.0 14.5 + - + +
224D VAL* 3.3 29.2 - - + -
282D CYS* 1.3 87.3 - - - +
284D ASP* 1.3 74.9 + - - +
285D ILE* 4.3 9.6 - - + -
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Residues in contact with ASP 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D PRO* 5.6 3.8 - - - +
57D MET* 5.1 1.9 - - - -
129D VAL* 3.4 15.4 - - + +
162D TYR 3.2 3.6 - - - -
163D HIS* 2.8 28.4 + - + +
282D CYS* 4.0 7.8 - - - -
283D VAL* 1.3 93.1 + - - +
285D ILE* 1.3 67.4 + - - +
286D MET* 3.4 2.4 + - - +
301D GLY* 3.0 23.9 - - - -
302D LEU 3.3 24.7 + - - +
304D ARG* 2.6 36.9 + - - +
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Residues in contact with ILE 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LEU* 5.2 8.1 - - + -
57D MET* 4.0 23.1 - - + -
96D PRO* 4.7 12.6 - - + -
160D SER 3.3 12.8 - - - +
161D GLN* 3.0 7.7 - - - +
162D TYR* 2.5 51.1 + - + +
163D HIS* 3.3 7.8 - - - -
224D VAL* 5.6 3.8 - - + -
283D VAL* 4.3 12.3 - - + -
284D ASP* 1.3 84.2 - - - +
286D MET* 1.3 59.9 + - - +
287D GLY 3.0 20.0 - - - +
299D TRP* 3.3 30.3 - - + +
300D ARG 3.7 5.2 - - - +
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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