Contacts of the strand formed by residues 249 - 255 (chain 1) in PDB entry 6Q8O
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 MET 249 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131 PHE* 4.3 6.7 - - + -
161 THR* 5.5 0.9 - - - -
171 LEU* 3.8 21.8 - - + -
651 ARG* 2.4 35.6 + - - -
2221 GLU* 3.6 0.7 - - - +
2261 SER* 3.3 32.9 + - - +
2291 PRO* 4.0 21.1 - - + -
2371 TRP* 5.1 4.3 - - + -
2381 PHE* 3.3 24.2 - - + -
2411 MET* 3.9 24.8 - - - +
2481 GLY* 1.3 74.9 - - - -
2501 LYS* 1.3 59.6 + - - +
2651 GLU* 4.5 13.5 - - + +
2661 LEU 3.7 16.6 - - - +
2671 PRO* 4.1 2.7 - - - -
2681 MET* 4.9 0.2 - - - -
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Residues in contact with LYS 250 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651 ARG* 3.9 18.4 - - - +
1021 LYS* 3.8 9.3 - - - +
2221 GLU* 3.1 38.7 + - - +
2491 MET* 1.3 76.3 - - - +
2511 LEU* 1.3 94.1 + - - +
2521 TYR* 3.4 20.1 + - + -
2651 GLU* 3.7 0.2 - - - -
2661 LEU 2.8 32.1 + - - +
2681 MET* 3.6 29.8 - - + -
3131 TYR* 5.6 2.9 - - - +
3231 LEU* 6.0 1.1 - - + -
3241 GLY 5.3 1.8 - - - -
3251 THR* 2.6 35.4 + - - +
3261 GLY* 4.2 3.3 - - - +
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Residues in contact with LEU 251 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 LEU* 3.5 30.3 - - + -
181 TYR* 3.5 35.9 - - + -
1021 LYS* 3.4 28.8 - - + +
1031 ASP* 4.8 0.2 - - - +
1061 ILE* 3.5 21.8 - - + -
2221 GLU* 4.0 11.3 + - + +
2501 LYS* 1.3 102.6 + - - +
2521 TYR* 1.3 54.6 + - - +
2531 GLN* 2.7 16.3 - - - +
2631 VAL* 4.5 4.5 - - + -
2641 TYR 3.7 4.9 - - - -
2651 GLU* 3.6 23.6 - - + -
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Residues in contact with TYR 252 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2501 LYS* 3.6 30.3 - - + +
2511 LEU* 1.3 71.4 - - - +
2531 GLN* 1.3 65.6 + - - +
2631 VAL* 3.4 2.3 - - - +
2641 TYR* 2.9 38.0 + - + +
2661 LEU* 3.7 18.6 - - + -
2671 PRO 3.6 18.6 - - - -
2681 MET* 3.1 38.0 - - - +
2691 GLY 3.5 6.9 + - - -
2701 THR* 4.8 4.7 + - - -
2751 LEU* 3.7 29.4 - - + -
3111 MET* 3.6 36.6 + - + +
3231 LEU* 4.3 8.1 - - + +
3261 GLY* 3.9 14.4 - - - +
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Residues in contact with GLN 253 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991 GLY 3.1 23.6 + - - +
1001 SER* 3.9 11.3 + - - +
1011 PHE* 3.6 24.7 - - + +
1021 LYS* 4.1 16.8 - - + +
2511 LEU 2.7 22.0 - - - +
2521 TYR* 1.3 76.0 - - - +
2541 ILE* 1.3 62.0 + - - +
2621 GLY 2.9 14.8 - - - +
2631 VAL* 4.3 5.6 - - + -
2641 TYR* 5.5 0.7 - - - -
2751 LEU* 5.9 1.8 - - - -
3251 THR* 3.1 24.1 + - - +
3261 GLY 2.7 19.5 + - - +
3271 GLY* 3.2 15.4 - - - +
3281 VAL* 2.9 15.3 + - - +
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Residues in contact with ILE 254 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011 PHE* 3.2 9.1 - - - -
2531 GLN* 1.3 75.5 - - - +
2551 SER* 1.3 66.9 - - - +
2581 VAL* 4.9 2.0 - - + -
2611 PRO* 3.5 12.8 - - + +
2621 GLY 2.9 42.5 + - - +
2641 TYR* 4.8 5.6 - - + -
2751 LEU* 4.6 18.2 - - + -
2761 ILE* 4.3 14.6 - - + -
2801 ALA* 4.1 26.5 - - + -
3281 VAL* 3.3 22.2 - - + +
3301 LEU* 3.6 37.7 - - + -
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Residues in contact with SER 255 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991 GLY* 4.4 0.7 - - - -
1011 PHE* 3.8 11.1 - - - -
2541 ILE* 1.3 77.3 - - - +
2561 GLY* 1.3 59.1 + - - +
2581 VAL* 5.7 0.9 - - - -
2611 PRO* 4.4 6.3 - - - -
3281 VAL 2.9 14.8 + - - -
3291 ILE* 3.2 21.8 - - - +
3301 LEU* 3.0 30.7 + - - +
872 SER* 3.5 7.3 + - - -
1282 CYS* 3.6 31.7 - - - +
1292 HIS* 5.1 0.4 - - - +
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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