Contacts of the strand formed by residues 207 - 215 (chain U) in PDB entry 1SC8
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 MET 207 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29U TRP* 3.9 22.0 - - + -
121U ILE* 3.5 25.9 - - + +
122U SER* 3.6 16.8 + - - -
137U GLU* 3.6 24.2 - - - +
200U VAL* 4.0 11.7 - - + -
201U CYS 3.7 3.1 - - - -
202U SER* 4.6 16.8 - - - -
206U ARG* 1.3 75.9 - - - +
208U THR* 1.3 60.2 + - - +
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Residues in contact with THR 208 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121U ILE* 4.3 2.9 - - - -
122U SER* 3.5 6.5 - - - +
123U LEU 3.7 3.1 - - - +
124U PRO* 3.4 44.9 - - + -
200U VAL* 3.4 5.7 - - - +
201U CYS 2.8 34.2 + - - -
203U LEU* 3.9 20.4 + - + +
206U ARG* 3.1 18.7 + - - +
207U MET* 1.3 75.7 + - - +
209U LEU* 1.3 63.1 + - - +
210U THR* 2.9 15.7 + - - +
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Residues in contact with LEU 209 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U SER* 4.1 6.7 - - - +
47U ILE* 4.1 12.1 - - + -
53U ILE* 3.5 33.2 - - + -
121U ILE* 3.8 22.9 - - + +
122U SER 2.9 18.2 + - - +
123U LEU* 4.4 11.2 - - + -
124U PRO* 3.2 18.0 - - - +
198U PRO* 3.6 23.8 - - + -
199U LEU 4.0 3.6 - - - +
200U VAL* 4.9 1.3 - - - +
208U THR* 1.3 68.1 - - - +
210U THR* 1.3 62.0 + - - +
211U GLY 3.2 28.3 - - - +
212U ILE* 4.9 2.9 - - + -
231U VAL* 3.4 19.0 - - + +
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Residues in contact with THR 210 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124U PRO* 4.3 6.8 - - - +
129U ASP* 4.0 15.9 - - - +
130U PRO* 4.0 19.5 - - + +
162U LEU* 4.9 2.5 - - + -
181U LEU* 3.4 29.6 - - + +
199U LEU* 3.0 8.6 + - + -
201U CYS* 3.3 37.9 - - - +
203U LEU* 5.7 0.5 - - - +
208U THR* 2.9 14.4 + - - +
209U LEU* 1.3 72.4 - - - +
211U GLY* 1.3 58.2 + - - +
231U VAL* 3.3 19.6 + - - +
232U SER 4.7 0.2 + - - -
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Residues in contact with GLY 211 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181U LEU* 5.0 0.4 - - - -
198U PRO* 3.7 0.3 - - - +
199U LEU* 2.8 42.0 + - - +
209U LEU* 3.2 12.3 - - - +
210U THR* 1.3 79.6 - - - +
212U ILE* 1.3 63.8 + - - -
228U TYR* 4.2 7.0 - - - -
229U THR 3.1 11.9 - - - -
231U VAL* 3.6 3.6 - - - -
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Residues in contact with ILE 212 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53U ILE* 3.7 21.8 - - + -
54U SER 3.4 25.4 - - - +
55U ALA* 4.1 4.9 - - + -
102U ASP 4.5 3.1 - - - +
103U ILE* 3.7 26.9 - - + -
196U GLY* 3.5 32.5 - - - +
197U GLY 3.4 4.5 - - - +
209U LEU* 4.9 6.5 - - + -
211U GLY* 1.3 79.4 - - - +
213U VAL* 1.3 71.1 + - - +
214U SER* 3.1 2.1 + - - -
228U TYR* 3.2 5.6 - - - +
229U THR* 3.0 35.6 + - - +
231U VAL* 4.1 11.4 - - + -
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Residues in contact with VAL 213 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U ALA* 4.2 2.9 - - - +
138U ILE* 4.8 10.1 - - + -
139U THR 5.3 2.0 - - - +
190U SER* 3.9 20.2 - - - +
194U ASP* 3.2 35.9 - - + +
195U SER* 3.4 5.7 - - - -
196U GLY 2.9 25.3 + - - +
197U GLY* 3.0 18.4 + - - +
198U PRO 5.0 1.1 - - - +
212U ILE* 1.3 72.7 - - - +
214U SER* 1.3 60.2 + - - +
227U VAL 5.4 0.2 - - - +
228U TYR* 3.6 25.3 - - + -
300U 2IN 3.6 27.8 - - + -
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Residues in contact with SER 214 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U ALA* 5.7 0.2 - - - -
57U HIS* 3.4 12.9 - - - -
99U HIS* 3.7 4.0 + - - +
102U ASP* 2.7 32.6 + - - +
212U ILE 3.1 7.4 + - - -
213U VAL* 1.3 76.1 - - - +
215U TRP* 1.3 80.3 + - - +
227U VAL* 3.2 13.5 + - - -
228U TYR 4.7 0.2 - - - -
229U THR* 3.9 16.1 + - - -
300U 2IN 3.0 24.3 + - - -
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Residues in contact with TRP 215 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97U LEU* 3.6 31.6 - - + -
98U ALA* 3.5 24.5 - - + -
99U HIS* 3.5 31.4 + - + +
172U TYR* 3.8 22.7 - + - -
175U GLU* 4.3 6.7 - - + -
176U VAL* 3.7 21.3 - - + -
180U MET* 3.8 10.9 - - - +
214U SER* 1.3 104.7 - - - +
216U GLY* 1.3 74.8 + - - +
226U GLY 3.7 0.9 - - - -
227U VAL* 2.7 74.6 + - + +
300U 2IN 3.0 32.8 - - - +
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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