Contacts of the strand formed by residues 237 - 246 (chain 7) in PDB entry 5U8T
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 GLN 237 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2463 GLY 4.8 2.2 + - - -
1077 GLN 3.1 15.3 - - - +
1087 GLN* 2.3 37.1 + - - +
1107 ALA* 3.7 3.7 - - - +
2337 ASP* 3.0 22.9 + - - +
2347 PHE* 3.1 43.0 + - - +
2357 LEU 3.9 1.8 - - - +
2367 GLY* 1.3 86.3 - - - +
2387 LEU* 1.3 62.7 + - - +
2397 ILE* 3.3 17.5 + - + +
3537 GLY 3.8 6.6 - - - +
3557 PHE* 3.8 13.9 + - - +
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Residues in contact with LEU 238 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827 LEU* 3.9 28.0 - - + -
1067 ILE* 4.4 11.9 - - + +
1077 GLN* 3.0 40.2 + - + +
1107 ALA* 3.1 21.4 - - + +
2047 PHE* 4.0 35.2 - - + -
2057 LYS 6.3 0.4 - - - -
2067 PRO* 6.2 0.2 - - + -
2217 SER 4.0 5.7 - - - +
2377 GLN* 1.3 69.8 - - - +
2397 ILE* 1.3 66.5 + - - +
3527 THR* 5.7 5.6 - - - -
3537 GLY 3.8 13.0 - - - +
3547 ILE* 4.1 17.0 - - + -
3797 GLN* 4.4 7.6 - - + -
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Residues in contact with ILE 239 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077 GLN* 5.0 1.3 - - + +
2217 SER* 4.2 16.8 - - - +
2237 LYS 5.6 0.2 - - - +
2257 LEU* 3.6 34.5 - - + -
2307 ILE* 4.8 2.9 - - + -
2347 PHE* 4.8 15.9 - - + -
2377 GLN* 3.3 30.0 + - + +
2387 LEU* 1.3 82.5 - - - +
2407 THR* 1.3 75.9 + - - +
2417 VAL* 3.7 13.6 + - + +
3517 VAL 4.0 0.7 - - - +
3527 THR* 3.1 6.3 - - - -
3537 GLY 2.9 31.3 + - - +
3557 PHE* 6.1 2.9 - - + -
3767 LEU* 5.7 1.9 - - + +
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Residues in contact with THR 240 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2067 PRO* 4.1 7.7 - - + +
2217 SER 4.5 2.6 + - - -
2227 SER* 3.0 37.1 + - - +
2237 LYS 3.1 20.1 + - - +
2247 PRO* 3.7 19.3 - - + -
2257 LEU 3.6 3.3 + - - -
2397 ILE* 1.3 82.5 - - - +
2417 VAL* 1.3 73.0 + - - +
3507 ASP* 4.3 14.4 - - + -
3517 VAL 4.3 0.4 - - - +
3527 THR* 3.3 27.7 - - + +
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Residues in contact with VAL 241 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2247 PRO* 4.1 4.5 - - - -
2257 LEU 3.8 13.7 - - - +
2277 VAL* 5.8 3.8 - - + -
2307 ILE* 4.0 23.1 - - + -
2397 ILE* 3.7 22.4 - - + +
2407 THR* 1.3 80.5 - - - +
2427 ARG* 1.3 62.0 + - - +
3157 ILE* 5.7 5.2 - - + -
3317 LEU* 6.0 2.2 - - + -
3337 ILE* 4.8 5.6 - - + -
3497 VAL 3.7 0.5 - - - +
3507 ASP* 3.9 0.5 - - - -
3517 VAL* 2.9 57.5 + - + +
3767 LEU* 4.2 17.9 - - + -
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Residues in contact with ARG 242 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2247 PRO* 3.2 48.6 + - + +
2257 LEU 4.0 3.7 + - - +
2267 SER* 5.3 1.0 - - - -
2277 VAL* 5.7 4.3 - - - +
2417 VAL* 1.3 78.0 - - - +
2437 GLY* 1.3 60.0 + - - +
3157 ILE* 4.5 6.2 - - - +
3167 GLN 4.6 1.0 - - - +
3177 GLU* 5.2 1.6 - - - -
3187 LEU* 4.5 18.6 - - + +
3217 GLN* 3.2 30.2 + - - +
3487 ILE* 5.5 6.1 - - + +
3497 VAL 3.4 13.0 - - - +
3507 ASP* 3.7 15.2 + - - +
3847 HIS* 4.7 16.5 + - + -
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Residues in contact with GLY 243 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2427 ARG* 1.3 78.2 - - - +
2447 ILE* 1.3 66.6 + - - -
3157 ILE* 3.5 14.0 - - - +
3167 GLN 3.2 13.0 - - - -
3187 LEU* 4.9 9.0 - - - -
3477 ASP 3.3 12.0 - - - +
3487 ILE* 3.5 15.3 - - - +
3497 VAL* 3.6 11.9 + - - +
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Residues in contact with ILE 244 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2437 GLY* 1.3 73.0 - - - -
2457 ILE* 1.3 74.7 + - - +
2467 THR* 4.3 5.2 - - - +
3157 ILE* 3.1 6.3 - - - -
3167 GLN* 2.9 43.4 + - + +
3177 GLU 3.4 25.4 - - - +
3187 LEU* 4.2 14.6 - - + +
3197 SER* 6.1 0.4 - - - -
3467 GLY* 3.5 22.0 - - - +
3477 ASP 3.8 4.7 - - - -
3487 ILE* 3.7 23.6 - - + -
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Residues in contact with ILE 245 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2447 ILE* 1.3 74.3 - - - +
2467 THR* 1.3 67.5 + - - +
2487 VAL* 3.6 30.1 - - + -
3137 CYS* 4.5 3.6 - - + -
3147 LYS 3.9 4.7 - - - +
3157 ILE* 3.5 27.6 - - + -
3437 LEU* 3.8 27.4 - - + -
3447 SER 3.1 31.4 - - - +
3457 PRO* 3.8 0.9 - - + -
3467 GLY* 2.6 26.5 + - - -
3477 ASP* 3.0 28.1 + - + +
3497 VAL* 4.1 7.4 - - + -
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Residues in contact with THR 246 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5023 ILE* 5.4 1.8 - - + -
5033 HIS* 4.4 23.2 - - + +
2447 ILE* 3.6 4.2 + - - +
2457 ILE* 1.3 79.8 + - - +
2477 ARG* 1.3 76.8 + - + +
2487 VAL 3.0 10.7 + - - -
3147 LYS* 2.9 38.4 + - + +
3167 GLN* 2.9 50.5 + - - +
3457 PRO* 5.7 0.2 - - - -
3467 GLY 4.8 0.7 - - - +
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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