Contacts of the strand formed by residues 207 - 215 (chain E) in PDB entry 1PPF
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 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A FUC 2.7 16.2 + - - -
29E PHE* 6.2 0.2 - - - -
122E GLN* 3.8 21.0 + - - +
200E VAL* 4.5 11.6 - - - +
201E CYS 3.2 0.6 - - - -
202E ASN* 1.3 76.9 - - - +
208E LEU* 1.3 66.6 + - - +
209E ILE* 5.4 1.9 - - - +
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Residues in contact with LEU 208 (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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122E GLN* 3.3 33.7 - - + +
123E LEU 4.3 3.8 - - - +
124E PRO* 4.3 22.0 - - + -
200E VAL* 3.4 2.6 - - - -
201E CYS 2.9 34.3 + - - +
202E ASN* 3.2 18.7 + - + +
207E GLY* 1.3 86.4 - - - +
209E ILE* 1.3 64.2 + - - +
210E HIS* 3.5 19.2 + - - +
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Residues in contact with ILE 209 (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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29E PHE* 4.1 17.7 - - + -
45E THR* 3.9 5.6 - - + -
53E MET* 4.0 20.0 - - + -
121E ALA* 3.5 32.1 - - + -
122E GLN 2.8 14.3 + - - +
123E LEU* 3.7 12.0 - - + +
124E PRO* 3.2 20.6 - - - +
198E PRO* 3.7 28.5 - - + -
199E LEU 3.7 2.0 - - - +
200E VAL* 4.1 13.5 - - + -
207E GLY 5.4 1.8 - - - +
208E LEU* 1.3 70.7 - - - +
210E HIS* 1.3 61.2 + - - +
211E GLY 3.7 18.8 - - - +
231E VAL* 3.4 11.8 - - + +
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Residues in contact with HIS 210 (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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124E PRO* 3.6 31.1 - - + +
128E ARG* 4.4 24.2 + - + +
130E LEU* 3.4 44.6 - - + +
181E VAL* 4.1 7.1 - - + +
199E LEU* 2.9 10.1 + - + -
201E CYS* 3.5 42.9 + - + -
202E ASN* 5.7 0.4 + - - -
208E LEU* 3.5 19.2 + - + +
209E ILE* 1.3 74.7 - - - +
211E GLY* 1.3 59.8 + - - +
229E ALA 3.7 1.0 - - - +
230E PRO* 3.7 5.0 - - - +
231E VAL* 3.0 23.8 + - - +
232E ALA* 4.5 4.8 + - - +
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Residues in contact with GLY 211 (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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181E VAL* 5.1 0.4 - - - -
198E PRO* 3.4 5.9 - - - +
199E LEU* 3.0 32.7 + - - +
209E ILE* 3.7 6.8 - - - +
210E HIS* 1.3 80.7 - - - +
212E ILE* 1.3 66.5 - - - +
228E PHE* 3.7 17.3 - - - -
229E ALA 3.0 10.3 - - - -
230E PRO* 4.9 0.2 - - - -
231E VAL* 3.8 2.2 - - - -
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Residues in contact with ILE 212 (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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45E THR* 5.9 1.1 - - - +
53E MET* 3.6 37.2 - - + -
54E SER 3.7 3.8 - - - +
55E ALA* 3.7 16.2 - - + +
102E ASP 4.6 1.1 - - - +
103E ILE* 3.7 31.4 - - + -
196E GLY* 3.4 34.1 - - - +
197E SER 3.6 4.3 - - - -
198E PRO* 5.9 0.4 - - + -
211E GLY* 1.3 79.3 - - - +
213E ALA* 1.3 70.0 + - - +
214E SER* 3.1 1.0 + - - -
228E PHE* 3.1 2.2 - - - -
229E ALA* 2.7 42.0 + - + +
231E VAL* 3.7 12.6 - - + -
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Residues in contact with ALA 213 (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 ALA* 4.1 3.6 - - - +
190E VAL* 4.6 12.6 - - + -
194E ASP 3.4 24.9 - - - +
195E SER* 3.4 6.1 - - - -
196E GLY* 2.7 26.9 + - - +
197E SER* 2.9 14.3 + - - +
212E ILE* 1.3 74.4 - - - +
214E SER* 1.3 59.7 - - - +
227E ALA 4.1 0.4 - - - -
228E PHE* 3.2 28.9 - - + -
18I LEU* 4.6 6.1 - - + -
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Residues in contact with SER 214 (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 ALA* 5.6 0.2 - - - -
57E HIS* 3.2 20.4 - - - -
99E LEU* 5.1 2.4 + - - +
102E ASP* 2.6 34.5 + - - +
180E ASN* 4.9 2.1 + - - -
195E SER* 3.8 0.7 + - - -
212E ILE 3.8 7.9 - - - -
213E ALA* 1.3 74.5 - - - +
215E PHE* 1.3 77.1 + - - +
227E ALA 3.0 15.5 + - - -
228E PHE 4.1 1.3 - - - -
229E ALA* 3.9 11.4 - - - -
17I THR* 3.6 2.4 - - - +
18I LEU* 3.4 15.0 + - - +
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Residues in contact with PHE 215 (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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99E LEU* 3.5 31.0 - - + -
177E ARG* 3.6 26.7 - - - -
180E ASN* 3.7 16.2 - - - -
214E SER* 1.3 93.0 - - - +
216E VAL* 1.4 67.6 + - - +
217E ARG* 4.0 25.1 - - - -
225E PRO 4.9 0.2 - - - +
226E ASP* 4.0 0.5 - - - -
227E ALA* 3.0 52.7 + - + +
15I ALA* 3.9 16.6 - - + -
16I CYS 3.1 22.9 - - - +
17I THR* 4.1 1.8 - - + +
18I LEU* 3.7 11.6 - - - +
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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