Contacts of the strand formed by residues 206 - 215 (chain A) in PDB entry 3MNS
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 GLN 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL* 4.3 30.2 - - + +
201A CYS 3.6 0.2 - - - +
202A LEU* 3.6 4.8 - - - +
203A VAL* 3.1 29.0 + - - +
204A ASN 4.4 4.0 - - - +
205A GLY* 1.3 79.4 - - - +
207A TYR* 1.3 71.2 + - - +
208A ALA* 3.5 7.5 + - - +
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Residues in contact with TYR 207 (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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27A TRP* 4.1 26.5 - + + -
122A VAL* 3.1 20.6 - - - +
135A PRO 5.3 2.0 - - - -
137A TYR* 3.6 24.0 - + - -
200A HIS* 3.9 28.7 - - + +
201A CYS 3.4 5.8 - - - -
202A LEU* 3.7 50.3 - - + +
206A GLN* 1.3 76.8 - - - +
208A ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 208 (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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122A VAL* 3.4 21.8 - - + +
123A LEU 4.3 1.8 - - - +
124A PRO* 4.3 12.1 - - + -
200A HIS* 3.4 4.6 - - - -
201A CYS 2.9 30.6 + - - +
203A VAL* 6.1 1.6 - - + -
206A GLN* 3.5 8.3 + - - +
207A TYR* 1.3 75.5 - - - +
209A VAL* 1.3 63.4 + - - +
210A HIS* 3.3 24.9 + - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 4.4 6.5 - - - +
45A THR* 3.9 26.5 - - + +
53A MET* 4.1 14.4 - - + -
121A GLY* 4.6 4.7 - - - -
122A VAL 2.9 19.0 + - - +
123A LEU* 4.1 7.4 - - + +
124A PRO* 3.1 18.8 - - - +
198A PRO* 3.7 16.6 - - + -
199A LEU 3.4 4.3 - - - +
200A HIS* 4.0 19.3 - - - +
208A ALA* 1.3 71.4 - - - +
210A HIS* 1.3 60.8 + - - +
211A GLY 3.6 21.8 - - - +
212A VAL* 5.5 0.2 - - + -
231A VAL* 3.6 8.5 - - - +
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Residues in contact with HIS 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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124A PRO* 3.7 29.3 - - + +
128A THR* 3.9 22.8 + - + +
130A LEU* 3.7 43.4 - - + +
181A VAL* 3.9 8.3 - - + +
199A LEU* 2.9 13.8 + - + +
201A CYS* 3.8 13.7 - - + -
203A VAL* 3.9 17.4 - - + +
208A ALA* 3.3 32.9 + - + +
209A VAL* 1.3 72.5 - - - +
211A GLY* 1.3 58.2 + - - +
230A ARG* 3.7 8.6 - - - +
231A VAL* 3.0 23.6 + - - -
232A SER* 4.6 1.2 + - - -
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Residues in contact with GLY 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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181A VAL* 5.1 0.4 - - - -
198A PRO* 3.4 6.9 - - - +
199A LEU* 2.9 34.9 + - - +
209A VAL* 3.5 7.4 - - - +
210A HIS* 1.3 83.1 - - - +
212A VAL* 1.3 64.0 + - - +
228A PHE* 3.8 14.8 - - - -
229A THR 3.3 8.5 - - - -
231A VAL* 4.0 1.1 - - - -
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Residues in contact with VAL 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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45A THR* 5.9 0.7 - - - +
53A MET* 3.8 29.2 - - + +
54A THR 3.7 4.9 - - - +
55A ALA* 3.7 27.8 - - + +
102A ASP 4.3 5.4 - - - +
103A ILE* 4.7 6.7 - - + -
196A GLY* 3.6 22.7 - - - +
197A GLY 3.4 4.0 - - - +
209A VAL* 5.5 0.2 - - + -
211A GLY* 1.3 71.9 - - - +
213A THR* 1.3 65.4 + - - +
214A SER 3.2 0.2 + - - -
228A PHE* 3.2 2.1 - - - -
229A THR* 2.8 43.7 + - - +
231A VAL* 3.8 18.4 - - + -
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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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55A ALA* 3.8 7.3 - - - +
138A ILE* 3.9 13.6 - - + +
190A GLY* 5.3 1.6 - - - -
191A CYS 5.7 0.9 - - - +
194A ASP* 3.5 29.7 + - + +
195A SER* 3.6 12.1 - - - +
196A GLY* 2.8 24.3 + - - +
197A GLY 2.8 19.8 + - - -
212A VAL* 1.3 70.8 - - - +
214A SER* 1.3 63.1 + - - +
215A PHE* 4.9 1.1 - - - +
216A VAL* 5.9 1.1 - - + -
226A THR* 4.1 23.1 - - + -
228A PHE* 3.2 23.6 - - + -
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Residues in contact with SER 214 (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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57A HIS* 3.0 23.7 + - - -
99A VAL* 3.5 7.8 + - - +
102A ASP* 2.7 29.0 + - - +
180A MET* 6.0 0.8 - - - +
195A SER* 4.1 3.8 + - - -
212A VAL 3.2 6.9 + - - -
213A THR* 1.3 76.1 - - - +
215A PHE* 1.3 78.5 + - - +
227A VAL* 2.8 17.7 + - - -
228A PHE 4.4 0.7 - - - -
229A THR* 4.0 14.8 - - - -
295A SO4 5.1 0.9 + - - -
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Residues in contact with PHE 215 (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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99A VAL* 3.8 39.0 - - + -
172A TRP* 3.8 31.0 - + - -
175A THR* 3.9 23.6 - - + -
176A VAL* 4.7 1.8 - - + -
180A MET* 4.2 16.2 - - + -
195A SER* 5.8 0.2 - - - -
213A THR* 4.9 2.1 - - - +
214A SER* 1.3 94.8 - - - +
216A VAL* 1.3 71.3 + - - +
226A THR* 4.0 1.0 - - - +
227A VAL* 2.9 70.1 + - + +
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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