Contacts of the strand formed by residues 277 - 285 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102E LYS* 4.2 11.4 - - - -
103E LEU 3.7 5.4 - - - -
104E GLN* 3.9 2.6 + - - +
169E GLY* 3.7 1.6 - - - +
273E CYS* 2.8 28.1 - - - +
274E LYS 3.5 1.3 + - - -
275E GLY* 2.9 8.3 + - - -
276E GLU* 1.3 79.2 - - - +
278E LEU* 1.3 62.5 + - - -
279E TYR* 3.5 26.5 - - - -
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Residues in contact with LEU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 5.0 5.4 - - + -
101E ALA 3.6 0.7 - - - +
102E LYS* 3.2 6.1 - - - +
103E LEU* 2.8 58.4 + - + +
105E LEU* 3.5 19.7 - - + -
122E ALA* 5.1 4.5 - - + -
167E VAL* 4.0 13.9 - - + -
168E GLY 3.6 9.9 - - - +
273E CYS* 4.1 9.0 - - - -
277E GLY* 1.3 73.4 - - - -
279E TYR* 1.3 76.3 + - - +
280E LEU* 3.6 30.5 - - + -
308E ILE* 4.3 20.6 - - + -
310E LEU* 4.4 16.8 - - + -
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Residues in contact with TYR 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E MET* 4.3 16.2 - - + -
101E ALA 3.6 4.5 - - - +
102E LYS* 3.3 33.7 + - + +
166E ALA 3.5 0.7 - - - +
167E VAL* 3.2 6.4 - - - -
168E GLY 2.8 45.7 + - - +
169E GLY 3.6 13.5 - - - -
170E GLU* 3.3 16.5 - - - +
171E PRO* 3.3 44.2 - - + +
237E THR* 4.4 1.1 - - + +
274E LYS 4.4 5.8 + - - -
275E GLY* 5.9 0.2 - - - -
277E GLY* 3.5 25.0 - - - -
278E LEU* 1.3 76.5 - - - +
280E LEU* 1.3 66.6 + - - +
281E SER* 3.8 7.5 + - - +
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Residues in contact with LEU 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ALA* 4.8 9.9 - - + -
53E LEU* 4.3 17.5 - - + -
100E MET* 3.3 3.6 - - - +
101E ALA 3.1 28.5 + - - +
103E LEU* 4.0 25.8 - - + -
166E ALA 3.5 3.4 - - - -
167E VAL* 4.0 17.9 - - + -
278E LEU* 3.6 25.8 - - + -
279E TYR* 1.3 81.7 - - - +
281E SER* 1.3 65.1 + - - +
306E PHE* 3.7 40.2 - - + -
308E ILE* 4.0 9.9 - - + -
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Residues in contact with SER 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU* 4.4 1.1 - - - +
98E TRP* 3.9 1.1 - - - -
99E SER 3.4 7.9 - - - -
100E MET* 4.0 1.8 - - - +
165E PHE* 2.9 4.0 - - - +
166E ALA* 2.7 41.7 + - - +
172E LEU* 4.1 24.8 + - - +
216E LEU* 3.8 26.1 - - - +
237E THR* 4.9 1.4 - - - +
279E TYR* 3.8 10.9 + - - +
280E LEU* 1.3 80.4 + - - +
282E CYS* 1.3 62.8 + - - +
306E PHE* 4.4 1.0 - - - -
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Residues in contact with CYS 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU* 3.5 29.2 - - - -
55E PRO* 6.5 0.7 - - - -
98E TRP* 3.3 10.7 - - - -
99E SER* 2.9 29.9 + - - +
164E VAL 3.0 16.6 - - - +
165E PHE* 3.2 10.5 - - + -
281E SER* 1.3 75.5 - - - +
283E VAL* 1.3 73.3 + - - +
284E ASP* 3.8 12.3 - - - -
304E ARG* 3.9 22.7 - - - +
306E PHE* 4.2 0.9 - - + -
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Residues in contact with VAL 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E PRO* 6.3 0.2 - - - -
97E THR 4.4 3.8 - - - +
98E TRP* 3.9 20.2 - - + -
99E SER* 4.7 4.0 - - - +
162E TYR* 3.2 33.2 - - + -
163E HIS* 2.8 21.0 - - - -
164E VAL* 2.9 20.6 + - + +
224E VAL* 3.5 30.5 - - + -
282E CYS* 1.3 79.3 - - - +
284E ASP* 1.3 75.1 + - - +
285E ILE* 3.7 10.3 - - + -
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Residues in contact with ASP 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E PRO* 5.3 6.3 - - - +
57E MET* 5.0 2.9 - - - -
129E VAL* 3.3 13.9 - - + +
162E TYR 3.5 0.2 - - - -
163E HIS* 2.8 26.6 + - + +
282E CYS* 3.8 13.9 - - - -
283E VAL* 1.3 89.2 - - - +
285E ILE* 1.3 65.1 + - - +
286E MET* 3.5 2.9 + - - +
301E GLY* 3.2 24.0 - - - -
302E LEU* 3.2 25.2 + - + +
303E PRO 4.7 0.2 - - - -
304E ARG* 2.5 39.4 + - - +
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Residues in contact with ILE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 5.0 8.3 - - + -
57E MET* 4.3 18.4 - - + -
96E PRO* 4.6 11.4 - - + -
160E SER 3.7 9.9 - - - +
161E GLN* 3.0 11.0 - - - +
162E TYR* 2.7 55.7 + - + +
163E HIS* 3.5 5.4 - - - -
224E VAL* 5.1 3.1 - - + -
283E VAL* 3.7 16.6 - - + -
284E ASP* 1.3 85.1 - - - +
286E MET* 1.3 60.7 + - - +
287E GLY 3.4 7.2 - - - +
299E TRP* 3.1 37.2 - - + +
300E ARG 3.9 4.7 - - - +
301E GLY* 4.6 0.9 - - - -
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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