Contacts of the strand formed by residues 208 - 215 (chain Z) in PDB entry 1SGF
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 VAL 208 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122Z THR* 5.0 2.2 - - - +
123Z LEU 4.9 4.0 - - - +
124Z PRO* 4.4 14.8 - - + -
125Z THR 5.4 0.7 - - - +
128Z GLU* 4.1 20.6 - - + +
200Z ILE* 3.9 3.6 - - - -
201Z CYS 3.0 32.6 + - - +
202Z ASP* 3.7 11.0 - - + +
207Z GLY* 1.3 83.2 - - - +
209Z LEU* 1.3 72.9 + - - +
210Z GLN* 3.2 18.2 + - + +
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Residues in contact with LEU 209 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Z VAL* 4.3 17.9 - - + -
47Z LEU* 4.5 9.6 - - + -
121Z ILE* 3.6 36.9 - - + +
122Z THR 3.8 19.4 + - - +
123Z LEU* 4.9 6.5 - - + -
124Z PRO* 3.0 28.9 - - + +
198Z PRO* 3.8 23.3 - - + -
199Z LEU 4.2 4.7 - - - +
200Z ILE* 4.3 7.0 - - + +
207Z GLY 4.2 1.0 + - - -
208Z VAL* 1.3 73.1 - - - +
210Z GLN* 1.3 58.8 + - - +
211Z GLY 3.6 24.2 - - - +
231Z LEU* 3.8 20.9 - - + -
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Residues in contact with GLN 210 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Z PRO* 3.7 17.1 - - - +
128Z GLU* 3.2 42.8 + - - +
130Z PRO* 3.5 40.5 - - + +
181Z LEU* 3.2 19.5 - - + +
199Z LEU 3.2 7.7 + - - +
201Z CYS* 4.4 15.7 - - + +
208Z VAL* 3.2 23.2 + - + +
209Z LEU* 1.3 73.0 - - - +
211Z GLY* 1.3 58.4 + - - +
230Z LYS* 4.7 0.8 - - - +
231Z LEU* 3.2 24.5 + - - +
232Z ASN* 4.1 6.9 - - - +
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Residues in contact with GLY 211 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181Z LEU* 4.4 4.5 - - - -
198Z PRO* 3.5 5.5 - - - +
199Z LEU* 2.8 44.9 + - - -
209Z LEU* 3.6 5.2 - - - +
210Z GLN* 1.3 82.2 - - - +
212Z ILE* 1.3 63.2 + - - +
228Z TYR* 4.7 0.7 - - - -
229Z THR 3.1 11.7 - - - -
231Z LEU* 4.0 6.1 - - - +
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Residues in contact with ILE 212 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Z VAL* 4.7 7.4 - - + -
53Z LEU* 3.3 45.3 - - + +
54Z THR 4.2 6.5 - - - +
55Z ALA* 4.2 12.3 - - + -
102Z ASP 4.9 2.2 - - - +
103Z LEU* 4.5 2.2 - - + -
196Z GLY* 3.7 32.5 - - - +
197Z GLY 3.2 9.4 - - - +
198Z PRO* 4.9 1.6 - - + -
211Z GLY* 1.3 78.1 - - - +
213Z THR* 1.3 67.1 + - - +
214Z SER 3.1 0.5 + - - -
228Z TYR* 3.5 3.3 - - - +
229Z THR* 2.8 43.8 + - + +
231Z LEU* 3.9 15.0 - - + +
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Residues in contact with THR 213 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Y ARG* 4.6 11.9 - - - +
55Z ALA* 4.3 1.7 - - - +
138Z ALA* 4.8 0.5 - - - +
139Z SER 5.4 1.9 + - - -
190Z THR* 3.3 37.5 - - + +
194Z ASP* 3.8 24.7 + - + +
195Z SER* 3.2 8.7 + - - +
196Z GLY 3.0 19.4 + - - -
197Z GLY 2.8 17.4 + - - -
198Z PRO 4.2 4.9 + - - -
212Z ILE* 1.3 72.4 - - - +
214Z SER* 1.3 60.3 + - - +
227Z VAL 5.1 1.1 - - - +
228Z TYR* 3.3 27.4 - - + -
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Residues in contact with SER 214 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Y THR* 5.3 0.2 - - - +
118Y ARG* 3.1 24.4 + - - +
55Z ALA* 5.6 0.7 - - - -
57Z HIS* 3.2 10.7 - - - -
99Z TYR* 4.5 1.7 + - - +
102Z ASP* 2.8 29.2 + - - +
195Z SER* 3.2 6.8 + - - -
212Z ILE 3.1 3.2 + - - -
213Z THR* 1.3 74.5 - - - +
215Z TRP* 1.3 78.4 + - - +
227Z VAL* 3.4 11.9 + - - -
228Z TYR* 4.5 0.7 - - - -
229Z THR* 3.8 23.8 - - - -
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Residues in contact with TRP 215 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y ALA* 3.0 25.1 - - + +
117Y THR* 4.1 3.8 - - + -
118Y ARG* 3.8 12.8 + - - +
99Z TYR* 3.9 27.7 - + + +
172Z HIS* 3.4 36.1 - + + -
174Z GLU* 3.2 49.4 - - + -
175Z LYS 3.3 22.0 - - - -
176Z VAL* 4.2 4.5 - - + -
180Z MET* 3.5 19.7 - - + +
213Z THR* 5.6 0.3 - - - +
214Z SER* 1.3 92.8 + - - +
216Z GLY* 1.3 75.6 + - - +
227Z VAL* 2.8 58.4 + - + +
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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