Contacts of the strand formed by residues 208 - 215 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G THR 5.3 3.4 - - - +
123G LEU 5.3 0.9 - - - +
124G PRO* 4.5 15.5 - - + -
125G THR* 5.3 2.5 - - - +
128G GLU* 4.8 13.7 - - + -
200G ILE* 3.6 2.0 - - - -
201G CYS 2.9 31.1 + - - +
202G ASP 2.7 16.1 + - - +
207G GLY* 1.3 78.8 - - - +
209G LEU* 1.3 73.5 + - - +
210G GLN* 3.4 16.7 + - - +
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Residues in contact with LEU 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G VAL* 4.3 13.0 - - + -
47G LEU* 4.4 15.9 - - + -
121G ILE* 3.8 35.6 - - + +
122G THR 4.0 18.3 + - - +
123G LEU* 4.8 5.8 - - + -
124G PRO* 2.8 32.4 - - + +
198G PRO* 3.8 23.1 - - + -
199G LEU 4.3 0.4 - - - +
200G ILE* 3.8 14.9 - - + +
207G GLY 4.0 1.4 + - - -
208G VAL* 1.3 75.0 - - - +
210G GLN* 1.3 53.6 + - - +
211G GLY 3.5 24.5 - - - +
231G LEU* 3.8 18.6 - - + -
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Residues in contact with GLN 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G PRO* 3.7 17.0 - - - +
128G GLU* 3.7 27.6 - - - +
130G PRO* 3.3 47.3 - - + +
181G LEU* 3.7 21.6 - - + +
199G LEU 3.1 9.2 + - - +
201G CYS* 4.0 18.9 + - + +
208G VAL* 3.4 17.6 + - - +
209G LEU* 1.3 79.1 - - - +
211G GLY* 1.3 59.3 + - - +
229G THR 3.6 0.7 - - - +
230G LYS* 5.0 0.7 - - - +
231G LEU* 3.0 29.6 + - - +
232G ASN* 4.4 4.5 + - - +
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Residues in contact with GLY 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G LEU* 4.6 4.3 - - - -
198G PRO* 3.5 1.7 - - - +
199G LEU* 2.9 37.1 + - - +
209G LEU* 3.5 13.7 - - - +
210G GLN* 1.3 83.0 - - - +
212G ILE* 1.3 60.4 + - - +
228G TYR* 5.0 0.2 - - - -
229G THR 3.1 13.5 - - - -
231G LEU* 3.7 8.6 - - - +
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Residues in contact with ILE 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G VAL* 5.0 5.8 - - + -
53G LEU* 3.4 39.5 - - + -
54G THR* 4.2 11.7 - - - +
55G ALA* 4.3 11.0 - - + -
102G ASP 4.6 1.3 - - - +
103G LEU* 3.8 17.0 - - + -
196G GLY* 3.9 20.2 - - - +
197G GLY 3.1 11.0 - - - +
198G PRO* 4.6 0.4 - - + -
199G LEU* 4.4 0.6 - - - +
211G GLY* 1.3 76.7 - - - +
213G THR* 1.3 74.3 + - - +
214G SER* 3.4 0.4 + - - -
228G TYR* 3.1 9.4 - - - +
229G THR* 2.8 43.1 + - - +
231G LEU* 4.2 7.4 - - + -
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Residues in contact with THR 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 5.1 7.0 - - - -
55G ALA* 4.3 1.9 - - - +
138G ALA* 4.7 0.5 - - - +
139G SER 5.3 1.2 + - - -
190G THR* 3.3 40.0 - - + +
194G ASP* 3.6 27.1 + - + +
195G SER* 3.3 9.9 + - - +
196G GLY 3.0 19.2 + - - -
197G GLY* 3.0 16.5 + - - -
198G PRO 4.2 5.7 + - - -
212G ILE* 1.3 74.7 - - - +
214G SER* 1.3 61.2 + - - +
215G TRP 5.7 1.1 - - - +
227G VAL 5.3 1.1 - - - +
228G TYR* 3.4 21.6 - - + -
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Residues in contact with SER 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 3.1 23.2 + - - +
55G ALA* 5.3 0.2 - - - -
57G HIS* 3.3 9.4 - - - -
99G TYR 4.4 1.0 + - - -
102G ASP* 2.7 31.7 + - - +
195G SER* 3.2 8.0 + - - -
212G ILE* 3.4 3.2 + - - -
213G THR* 1.3 74.5 - - - +
215G TRP* 1.3 76.3 + - - +
227G VAL* 3.4 12.6 + - - -
228G TYR* 4.6 1.1 - - - -
229G THR* 3.7 23.3 - - - -
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Residues in contact with TRP 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 3.4 26.9 - - + +
117B THR* 3.9 4.5 - - + +
118B ARG* 4.1 8.7 + - - +
99G TYR* 4.1 24.8 - + + +
172G HIS* 3.6 37.0 - + + -
174G GLU* 3.2 49.6 - - + -
175G LYS 3.4 20.4 - - - -
176G VAL* 4.0 5.6 - - + -
180G MET* 3.4 16.0 - - + +
190G THR* 5.5 0.7 + - - -
213G THR* 5.7 1.0 - - - +
214G SER* 1.3 93.2 + - - +
216G GLY* 1.3 75.4 + - - +
226G GLY* 3.9 1.6 - - - -
227G VAL* 2.9 60.9 + - + +
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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