Contacts of the strand formed by residues 207 - 213 (chain A) in PDB entry 6S1M
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 SER 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A SER* 3.5 4.6 + - - -
195A ARG 2.9 33.2 + - - +
196A GLU* 6.1 0.8 - - - +
205A GLY 4.5 2.9 + - - -
206A PRO* 1.3 78.2 + - - +
208A PRO* 1.3 77.3 - - - +
209A PHE* 3.2 11.1 - - - -
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Residues in contact with PRO 208 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A PRO* 4.4 2.9 - - - +
152A ALA* 3.7 24.4 + - + +
159A GLU* 5.6 10.1 - - + +
192A LEU* 4.9 18.2 - - + -
193A CYS 3.4 9.0 - - - +
194A SER* 4.5 2.9 - - - -
207A SER* 1.3 89.1 - - - +
209A PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 4.6 7.0 - - + -
150A THR* 3.8 7.2 - - - +
151A PRO* 3.8 35.0 - - + -
152A ALA* 4.2 2.2 - - - +
192A LEU* 3.8 4.2 - - - +
193A CYS* 2.8 44.7 + - - +
195A ARG* 3.3 35.4 - - + -
196A GLU* 3.8 10.1 - - - -
197A SER* 3.8 23.6 - - - -
207A SER* 3.2 29.8 - - - -
208A PRO* 1.3 75.4 - - - +
210A LEU* 1.3 65.4 + - - +
245A GLU* 4.2 9.2 - - - -
569A LEU* 3.9 19.7 - - + -
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 3.3 7.8 - - - +
150A THR* 2.8 40.3 + - + +
151A PRO 4.8 2.0 - - - +
152A ALA* 3.8 23.1 - - + -
158A PRO* 4.3 17.3 - - + +
164A LEU* 4.4 10.1 - - + -
167A GLU* 3.4 26.9 - - - +
190A VAL* 4.9 7.0 - - + -
191A GLU 3.3 13.9 - - - +
192A LEU* 3.7 22.9 - - + -
209A PHE* 1.3 73.3 - - - +
211A ARG* 1.3 61.5 + - - +
212A ILE* 3.9 16.8 + - + +
232A ARG* 4.9 9.9 - - - +
238A THR* 4.9 2.0 - - + -
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 3.6 43.2 + - + -
148A PHE 3.7 9.4 - - - +
149A TYR* 3.4 40.0 + - + -
189A ALA 4.4 2.9 - - - +
190A VAL* 4.2 2.1 - - - -
191A GLU* 3.2 63.8 + - + +
193A CYS* 4.0 6.5 - - - -
195A ARG* 5.6 1.4 - - - +
209A PHE 4.0 1.6 + - - -
210A LEU* 1.3 70.5 - - - +
212A ILE* 1.3 65.7 + - - +
213A THR* 3.9 15.9 + - + +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 3.3 2.7 - - - -
148A PHE* 2.9 56.6 + - + +
150A THR* 4.3 24.9 - - - +
167A GLU* 5.8 2.7 - - - +
188A LEU* 3.8 23.1 - - + +
189A ALA 4.5 6.7 - - - +
210A LEU* 4.3 19.1 - - + +
211A ARG* 1.3 74.8 - - - +
213A THR* 1.3 73.5 + - - +
214A VAL* 4.5 2.6 - - + +
227A LEU* 4.4 20.6 - - + -
232A ARG* 4.8 6.1 - - - +
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Residues in contact with THR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA* 5.6 5.2 - - - -
146A PRO 4.1 4.0 - - - -
147A TYR* 3.7 15.9 - - + -
187A VAL* 2.7 18.0 + - - +
188A LEU* 2.6 52.7 + - - +
189A ALA* 3.9 9.7 - - + +
191A GLU* 5.1 7.0 - - - +
211A ARG* 4.5 21.8 - - + +
212A ILE* 1.3 77.1 - - - +
214A VAL* 1.3 62.4 + - - +
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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