Contacts of the strand formed by residues 206 - 213 (chain H) in PDB entry 1PPB
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 ARG 206 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122H CYS* 4.0 7.4 - - - -
202H LYS* 4.5 0.4 - - - -
203H SER* 3.1 22.3 + - - -
204H ASN* 3.5 31.9 - - + +
205H ASN* 1.3 77.8 - - - +
207H TRP* 1.3 64.4 + - - +
208H TYR* 3.4 22.7 + - + -
1L CYS* 3.4 81.1 + - - +
2L GLY 3.4 5.8 - - - -
3L LEU* 4.0 24.2 - - + +
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Residues in contact with TRP 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H TRP* 3.5 34.1 - + + -
121H VAL* 3.6 4.7 - - + +
122H CYS* 3.3 22.3 + - - +
137H ARG* 3.1 35.9 - - + -
200H VAL* 3.8 26.7 - - + -
201H MET* 3.5 9.0 - - - -
202H LYS* 3.8 37.9 - - + +
206H ARG* 1.3 75.3 - - - +
208H TYR* 1.3 57.4 + - - +
2L GLY* 3.1 25.9 + - - +
4L ARG* 3.4 19.7 - - - +
8L GLU* 3.2 26.6 + - - -
14L ASP* 3.4 40.4 - - + -
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Residues in contact with TYR 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H VAL* 3.8 3.6 - - - -
122H CYS* 3.3 22.0 - - + +
123H LEU 3.3 27.8 - - - -
124H PRO* 3.5 15.9 - - + -
125H ASP* 4.4 11.2 + - - -
128H THR* 4.0 20.5 + - + -
129H LEU* 5.5 0.2 - - - -
200H VAL* 3.2 2.9 - - - -
201H MET 2.9 31.7 + - - +
203H SER* 3.9 11.0 - - - -
204H ASN* 3.4 32.8 - + - +
206H ARG* 3.4 35.6 + - + -
207H TRP* 1.3 74.7 - - - +
209H GLN* 1.3 60.8 + - - +
210H MET* 3.3 22.8 + - + +
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Residues in contact with GLN 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H SER* 2.8 29.9 + - - -
47H ILE* 4.3 0.5 - - - +
53H LEU* 3.6 15.9 + - - +
121H VAL* 3.5 18.0 - - + +
122H CYS 2.8 16.6 + - - +
123H LEU* 4.5 4.5 - - + -
124H PRO* 3.0 23.5 - - - +
196H GLY 5.0 0.8 + - - -
197H GLY 4.6 0.6 + - - -
198H PRO* 3.6 19.3 - - + +
199H PHE 3.7 6.5 - - - +
200H VAL* 4.1 4.0 - - + -
208H TYR* 1.3 68.5 - - - +
210H MET* 1.3 59.9 + - - +
211H GLY 3.0 28.2 + - - +
212H ILE* 3.3 23.2 - - - +
231H VAL* 3.7 10.7 - - + +
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Residues in contact with MET 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H PRO* 3.4 30.5 - - + -
128H THR* 4.6 2.5 - - + +
129H ALA* 4.2 21.1 - - + +
130H LEU* 3.6 33.0 - - + +
181H PHE* 3.3 11.6 - - - -
199H PHE* 2.8 16.7 + - + +
201H MET* 3.5 41.7 - - + -
208H TYR* 3.3 37.1 + - + +
209H GLN* 1.3 73.2 - - - +
211H GLY* 1.3 57.6 + - - +
230H HIS* 4.1 1.4 + - - -
231H VAL* 3.2 23.1 + - - +
232H PHE 4.5 1.7 + - - -
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Residues in contact with GLY 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H PHE* 3.7 12.6 - - - -
199H PHE* 2.8 36.3 + - - +
209H GLN* 3.0 14.2 + - - +
210H MET* 1.3 80.8 - - - +
212H ILE* 1.3 65.8 + - - -
228H TYR* 4.6 0.7 - - - -
229H THR 3.1 11.9 - - - -
231H VAL* 3.6 2.2 - - - -
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Residues in contact with ILE 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LEU* 4.0 13.5 - - + -
54H THR* 3.8 10.8 - - - +
55H ALA* 3.9 13.2 - - + +
102H ASP 4.0 6.1 - - - +
103H ILE* 3.6 36.3 - - + -
196H GLY* 3.5 33.7 - - - +
197H GLY 3.5 2.5 - - - -
209H GLN* 3.3 19.5 - - - +
211H GLY* 1.3 73.9 - - - -
213H VAL* 1.3 66.8 + - - +
214H SER 3.0 1.6 + - - -
228H TYR* 3.3 6.4 - - - -
229H THR* 3.0 37.4 + - - +
231H VAL* 3.9 8.3 - - + -
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Residues in contact with VAL 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H 0G6 4.2 15.0 - - + +
55H ALA* 4.1 2.4 - - - +
138H VAL* 3.4 33.7 - - + -
139H THR 5.2 0.2 - - - +
190H ALA* 3.6 23.6 - - + -
194H ASP* 3.2 35.0 - - + +
195H SER* 3.2 10.1 - - - +
196H GLY 2.9 19.9 + - - -
197H GLY* 2.8 21.6 + - - +
198H PRO 5.2 0.4 - - - +
212H ILE* 1.3 71.0 - - - +
214H SER* 1.3 58.9 + - - +
227H PHE 5.2 0.9 - - - +
228H TYR* 3.9 14.5 - - + -
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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