Contacts of the strand formed by residues 209 - 216 (chain A) in PDB entry 1P01
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 ALA 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.6 22.9 - - + -
124A VAL* 4.2 4.0 - - + -
126A GLY 2.8 17.9 + - - +
127A SER* 3.5 21.5 - - - +
128A THR 5.0 0.2 - - - -
129A GLU* 5.6 0.2 - - - -
199A TRP 3.8 6.7 - - - -
200A ILE* 4.1 4.5 - - + +
207A GLY 3.5 2.2 + - - -
208A GLN* 1.3 71.5 - - - +
210A GLN* 1.3 62.2 + - - +
211A GLY 3.9 0.7 - - - -
231A LEU* 3.4 25.6 - - + +
241A LEU* 4.0 9.0 - - + -
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Residues in contact with GLN 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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128A THR 2.8 25.6 + - - -
129A GLU* 3.6 13.2 - - - +
130A ALA* 2.8 34.3 + - + +
136A VAL* 4.0 21.5 - - + -
162A ILE* 4.5 4.6 - - + +
199A TRP* 2.8 20.6 + - + +
200A ILE* 4.4 0.2 - - - -
201A THR* 3.8 7.2 - - + +
208A GLN* 3.1 26.7 + - - +
209A ALA* 1.3 75.8 + - - +
211A GLY* 1.4 57.0 + - - +
228A PHE* 3.6 25.7 - - + -
230A ARG* 3.6 8.1 - - - +
231A LEU* 2.9 20.4 + - - +
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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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46A PHE* 3.4 12.2 - - - -
198A SER 3.7 0.2 - - - -
199A TRP* 2.9 29.1 + - - +
209A ALA 3.9 1.0 - - - -
210A GLN* 1.4 82.7 - - - +
212A VAL* 1.3 66.3 - - - -
228A PHE* 3.8 5.2 - - - -
229A GLU 3.0 13.9 - - - -
231A LEU* 3.6 14.2 - - - +
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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 GLY* 4.1 13.7 - - - -
46A PHE* 4.5 2.9 - - + -
53A VAL* 4.1 20.9 - - + -
54A THR* 3.9 23.1 - - - +
55A ALA* 4.5 2.9 - - + +
102A ASP 4.4 4.9 - - - +
196A GLY* 3.6 22.4 - - - +
197A GLY 3.2 4.3 - - - -
211A GLY* 1.3 79.5 - - - +
213A MET* 1.3 62.8 + - - +
214A SER 3.4 0.2 + - - -
228A PHE* 3.3 4.2 - - - -
229A GLU* 2.8 47.6 + - + +
231A LEU* 5.2 0.9 - - + -
234A ILE* 4.0 13.5 - - + -
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Residues in contact with MET 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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4A 0EG 3.7 17.5 - - + -
55A ALA* 3.6 10.2 - - - +
138A ARG* 3.9 11.7 - - - +
192A MET* 3.8 36.6 - - + +
194A ASP* 3.4 27.1 - - - +
195A SER* 3.6 1.6 - - - -
196A GLY 2.7 23.8 + - - +
197A GLY 2.9 15.5 + - - +
199A TRP* 3.5 25.8 - - + +
212A VAL* 1.3 72.4 - - - +
214A SER* 1.3 57.9 + - - +
215A GLY 3.3 21.8 - - - +
226A SER 4.1 3.1 - - - -
227A LEU 3.2 34.1 - - - +
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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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4A 0EG 3.2 12.2 + - - -
57A HIS* 3.0 24.8 - - - -
102A ASP* 2.6 33.1 + - - +
171A TYR* 2.7 24.7 + - - -
180A LEU* 4.2 19.1 - - - +
195A SER* 3.8 0.9 + - - -
212A VAL 3.4 2.6 + - - -
213A MET* 1.3 74.0 - - - +
215A GLY* 1.3 58.9 + - - +
227A LEU 2.9 20.1 + - - -
228A PHE* 4.5 1.8 - - - -
229A GLU* 4.6 1.6 - - - -
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Residues in contact with GLY 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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4A 0EG 3.2 24.0 - - - -
171A TYR* 3.1 12.7 + - - -
192A MET* 4.2 2.5 - - - -
213A MET* 3.3 9.9 - - - +
214A SER* 1.3 84.5 - - - +
216A GLY* 1.3 54.4 + - - -
226A SER 3.6 0.2 - - - -
227A LEU* 2.7 34.0 + - - +
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Residues in contact with GLY 216 (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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4A 0EG 2.9 42.5 + - - +
171A TYR* 4.5 0.8 + - - -
192A MET* 3.4 12.2 - - - +
215A GLY* 1.3 74.3 - - - -
217A ASN* 1.3 72.9 + - - +
225A SER 3.0 14.6 - - - -
227A LEU* 4.8 3.4 - - - -
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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