Contacts of the strand formed by residues 207 - 215 (chain E) in PDB entry 1SFQ
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 TRP 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D GLY* 2.9 29.5 + - - +
4D ARG* 3.3 22.5 - - - +
8D GLU* 2.9 24.9 + - - -
14D ASP* 3.5 40.8 - - + -
29E TRP* 3.4 36.3 - + + -
121E VAL* 3.4 3.4 - - + +
122E CYS* 3.1 28.4 + - - +
137E ARG* 3.3 31.9 - - - -
200E VAL* 3.5 32.1 - - + -
201E MET* 3.6 14.6 - - - -
202E LYS* 3.8 27.2 - - + +
206E ARG* 1.3 75.4 - - - +
208E TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 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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121E VAL* 4.1 3.1 - - - -
122E CYS* 3.3 21.0 - - + -
123E LEU 3.4 26.0 - - - -
124E PRO* 3.7 9.9 - - + -
125E ASP* 4.5 9.4 + - - -
128E THR* 3.8 28.7 + - + -
129E LEU* 5.1 1.3 - - - +
200E VAL* 3.2 4.3 - - - -
201E MET 2.9 36.4 + - - +
203E SER* 3.5 25.8 - - - -
204E ASN* 2.9 24.3 - + - +
206E ARG* 3.5 23.6 - - + -
207E TRP* 1.3 74.3 - - - +
209E GLN* 1.3 61.3 + - - +
210E MET* 3.4 20.7 + - - +
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Residues in contact with GLN 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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45E SER* 2.6 34.7 + - - -
47E ILE* 4.5 2.0 - - - +
53E LEU* 3.9 17.1 - - - +
121E VAL* 3.7 23.7 - - + +
122E CYS 2.9 12.6 + - - +
123E LEU* 4.7 3.6 - - + +
124E PRO* 3.2 20.8 - - - +
196E GLY 4.9 1.2 - - - +
197E GLY 4.6 0.7 - - - +
198E PRO* 3.4 22.5 - - + +
199E PHE 3.6 3.8 - - - +
200E VAL* 4.0 3.8 - - + -
208E TYR* 1.3 72.2 - - - +
210E MET* 1.3 59.6 + - - +
211E GLY 2.9 27.1 - - - +
212E ILE* 3.6 15.8 - - - +
231E VAL* 3.6 8.9 - - + +
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Residues in contact with MET 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* 3.7 27.1 - - + -
128E THR* 4.5 7.6 - - - +
129E LEU* 3.6 35.4 - - + +
130E LEU* 3.7 31.9 - - + +
181E PHE* 3.4 10.5 - - + -
199E PHE* 2.9 14.1 + - + +
201E MET* 3.4 39.0 - - + +
208E TYR* 3.9 19.7 - - - +
209E GLN* 1.3 73.5 - - - +
211E GLY* 1.3 58.1 + - - +
230E HIS* 4.0 2.3 + - - -
231E VAL* 3.1 23.6 + - - +
232E PHE* 4.4 2.5 + - + -
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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 PHE* 3.6 14.6 - - - -
199E PHE* 2.9 29.5 + - - +
209E GLN* 2.9 17.9 - - - +
210E MET* 1.3 81.4 - - - +
212E ILE* 1.3 64.2 + - - -
229E THR 3.1 11.7 - - - -
231E VAL* 3.7 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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53E LEU* 4.0 12.3 - - + -
54E THR* 3.8 8.5 - - - +
55E ALA* 3.9 12.6 - - + +
102E ASP 4.1 1.1 - - - +
103E ILE* 3.5 38.8 - - + -
196E GLY* 3.4 38.1 - - - +
197E GLY 3.4 3.4 - - - -
209E GLN* 3.6 13.0 - - - +
211E GLY* 1.3 77.4 - - - -
213E VAL* 1.3 69.9 + - - +
214E SER* 3.1 1.4 + - - -
228E TYR* 3.2 6.4 - - - +
229E THR* 2.8 43.2 + - - +
231E VAL* 3.8 9.0 - - + -
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Residues in contact with VAL 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* 3.8 3.6 - - - +
138E VAL* 3.5 31.0 - - + -
190E ALA* 3.8 21.1 - - + -
194E ASP* 3.3 21.1 - - + +
195E SER* 3.4 22.1 - - - +
196E GLY 3.0 21.5 + - - -
197E GLY* 2.9 22.7 + - - +
198E PRO 5.1 0.4 - - - +
212E ILE* 1.3 73.5 - - - +
214E SER* 1.3 60.4 + - - +
227E PHE 5.1 0.7 - - - +
228E TYR* 3.6 18.0 - - + -
301E 0G6 4.1 15.0 - - + +
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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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57E HIS* 3.0 11.5 + - - -
99E LEU* 3.9 2.3 + - - +
102E ASP* 2.7 33.5 + - - +
180E MET* 6.1 1.1 - - - +
195E SER* 4.2 0.9 - - - -
212E ILE 3.1 2.6 + - - -
213E VAL* 1.3 76.0 - - - +
215E TRP* 1.3 79.7 + - - +
227E PHE 3.1 14.1 + - - -
228E TYR* 4.2 1.3 - - - -
229E THR* 3.7 21.3 - - - -
301E 0G6 2.9 23.9 + - - -
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Residues in contact with TRP 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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98E ASN 4.0 4.6 + - - -
99E LEU* 3.9 15.5 - - + -
172E THR* 4.1 14.4 - - + -
174E ILE* 3.5 42.8 - - + -
176E ILE* 4.2 4.3 - - + -
180E MET* 3.5 31.4 - - + +
214E SER* 1.3 107.3 - - - +
216E GLY* 1.3 77.6 + - - +
217E GLU* 4.4 6.1 - - + -
226E GLY 3.8 0.5 - - - -
227E PHE* 2.8 81.2 + + + +
301E 0G6 3.2 55.7 + + + +
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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