Contacts of the helix formed by residues 251 - 268 (chain 2) in PDB entry 5IY8
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 251 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2042 LEU* 3.6 15.3 - - + -
2462 GLY* 3.5 13.6 - - - +
2492 TYR* 3.0 27.8 + - + -
2502 SER* 1.3 78.9 - - - +
2522 GLU* 1.3 60.8 + - - +
2532 GLY 4.0 1.3 - - - +
2542 MET* 3.0 56.2 - - + +
2552 SER* 3.3 15.6 + - - -
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Residues in contact with GLU 252 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2502 SER* 3.7 8.9 + - - +
2512 VAL* 1.3 70.4 - - - +
2532 GLY* 1.3 67.0 + - - +
2552 SER* 2.6 26.0 + - - +
2562 ASP* 3.0 19.2 + - - +
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Residues in contact with GLY 253 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2042 LEU* 4.9 12.0 - - - +
2512 VAL* 3.3 4.1 - - - +
2522 GLU* 1.3 80.3 - - - +
2542 MET* 1.3 61.0 + - - +
2562 ASP* 3.4 9.3 + - - +
2572 SER* 3.2 23.8 + - - -
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Residues in contact with MET 254 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002 GLY* 4.5 7.9 - - - +
2022 GLN 3.5 18.4 - - - +
2032 PHE* 4.9 0.7 - - + -
2042 LEU* 3.4 23.5 - - + +
2072 ASP* 3.0 30.1 - - + +
2112 GLN* 4.5 2.9 + - - +
2422 PHE* 3.5 36.6 - - + -
2462 GLY* 4.8 10.5 - - - -
2512 VAL* 3.0 36.2 - - + +
2522 GLU 3.2 0.6 - - - -
2532 GLY* 1.3 76.4 - - - +
2552 SER* 1.3 62.1 + - - +
2572 SER* 3.1 18.1 + - - -
2582 LEU* 3.1 11.1 + - - +
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Residues in contact with SER 255 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2432 SER* 5.7 8.1 - - - +
2462 GLY 5.5 3.5 - - - -
2472 LYS* 5.4 16.4 - - - -
2512 VAL 3.3 9.5 + - - -
2522 GLU* 2.6 26.3 + - - +
2542 MET* 1.3 77.6 - - - +
2562 ASP* 1.3 69.0 + - - +
2582 LEU* 2.9 21.2 + - - +
2592 LEU* 3.0 13.7 + - - +
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Residues in contact with ASP 256 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2522 GLU* 3.0 19.9 + - - +
2532 GLY* 3.7 9.2 - - - +
2542 MET 3.2 0.2 - - - -
2552 SER* 1.3 89.2 + - - +
2572 SER* 1.3 61.8 + - - +
2592 LEU* 2.7 41.6 - - + +
2602 ASN* 2.8 15.0 + - - +
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Residues in contact with SER 257 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2072 ASP* 4.9 2.8 - - - +
2082 THR* 4.6 9.7 + - - -
2112 GLN* 3.0 43.9 - - - +
2532 GLY 3.2 11.7 + - - -
2542 MET* 3.1 9.9 + - - -
2562 ASP* 1.3 79.8 - - - +
2582 LEU* 1.3 59.5 + - - +
2602 ASN* 3.2 11.7 + - - +
2612 PHE* 2.8 29.0 + - - -
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Residues in contact with LEU 258 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2112 GLN* 4.1 1.3 - - - +
2362 PHE* 2.9 34.3 - - + -
2392 GLN* 3.3 24.2 - - + +
2402 LEU* 4.8 3.8 - - + +
2422 PHE* 5.7 4.7 - - + -
2432 SER* 2.9 40.4 - - - +
2542 MET 3.1 9.1 + - - +
2552 SER* 2.9 15.0 + - - +
2572 SER* 1.3 76.8 - - - +
2592 LEU* 1.3 58.7 + - - +
2612 PHE* 2.9 17.3 + - - +
2622 LEU* 2.7 38.1 + - + +
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Residues in contact with LEU 259 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2552 SER 3.0 9.1 + - - +
2562 ASP* 2.7 41.3 + - + +
2582 LEU* 1.3 78.0 - - - +
2602 ASN* 1.3 96.8 + - - +
2622 LEU* 3.1 11.7 + - - +
2632 GLN* 2.7 41.7 + - - +
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Residues in contact with ASN 260 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2112 GLN* 5.9 2.5 - - + -
2152 PHE* 4.1 16.6 - - + -
2562 ASP* 2.8 24.2 + - - +
2572 SER* 3.4 11.1 - - - +
2582 LEU 3.1 0.2 - - - -
2592 LEU* 1.3 96.6 - - - +
2612 PHE* 1.3 58.5 + - + +
2632 GLN* 3.9 10.8 - - - +
2642 HIS* 2.8 33.8 + - - +
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Residues in contact with PHE 261 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1942 PRO* 6.2 2.0 - - + -
1972 THR* 4.5 4.3 - - - -
2102 ALA 4.0 1.6 - - - -
2112 GLN* 2.9 70.7 - - + -
2142 TYR* 2.9 51.0 - + + -
2152 PHE* 5.6 1.3 - - + +
2362 PHE* 2.9 24.9 - + + -
2392 GLN* 2.7 30.3 - - - -
2572 SER 2.8 25.4 + - - -
2582 LEU 2.9 4.1 + - - +
2602 ASN* 1.3 80.1 - - + +
2622 LEU* 1.3 57.8 + - - +
2642 HIS* 3.3 1.4 + - - -
2652 LEU* 2.8 30.4 + - - +
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Residues in contact with LEU 262 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2362 PHE* 2.9 43.3 - - + -
2372 LEU* 6.2 1.3 - - + -
2402 LEU* 5.1 6.7 - - + -
2582 LEU* 2.7 52.4 + - + +
2592 LEU* 3.1 8.5 + - - +
2612 PHE* 1.3 78.5 - - - +
2632 GLN* 1.3 65.3 + - - +
2652 LEU* 2.9 10.7 + - + +
2662 ARG* 2.9 29.8 + - + +
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Residues in contact with GLN 263 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152 PHE* 6.3 0.9 - - + -
2592 LEU* 2.7 35.8 + - - +
2602 ASN* 3.9 10.2 - - - +
2622 LEU* 1.3 74.1 - - - +
2642 HIS* 1.3 65.3 + - - +
2662 ARG* 3.2 8.3 + - + +
2672 GLU* 2.9 24.9 + - + +
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Residues in contact with HIS 264 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2142 TYR* 5.1 0.2 - - + -
2152 PHE* 2.9 70.5 + + + -
2182 GLN* 3.0 34.3 - - + +
2192 TYR* 2.7 45.5 + + + -
2602 ASN 2.8 10.7 + - - +
2612 PHE* 3.8 3.4 - - - +
2632 GLN* 1.3 78.8 - - - +
2652 LEU* 1.3 63.9 + - - +
2672 GLU* 3.1 17.8 + - + +
2682 PHE* 2.9 21.7 + - + +
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Residues in contact with LEU 265 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2142 TYR* 3.1 23.1 - - - +
2182 GLN* 2.6 37.8 - - - +
2302 LEU* 4.5 9.0 - - + -
2332 ILE* 3.7 13.5 - - + +
2342 LEU* 5.2 5.6 - - - +
2362 PHE* 4.5 20.0 - - + -
2372 LEU* 4.8 13.9 - - + -
2612 PHE 2.8 15.2 + - - +
2622 LEU* 3.3 13.0 - - + +
2642 HIS* 1.3 75.5 - - - +
2662 ARG* 1.3 62.4 + - + +
2682 PHE 2.6 17.1 + - - +
2692 GLY* 4.5 1.4 - - - -
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Residues in contact with ARG 266 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2622 LEU* 2.9 22.6 + - + +
2632 GLN* 3.6 9.0 - - + +
2652 LEU* 1.3 79.2 - - + +
2672 GLU* 1.3 58.5 + - - +
2692 GLY 5.3 0.4 - - - -
2702 LEU* 2.8 50.2 + - + +
2732 GLN* 2.7 42.1 + - - +
2742 ARG 4.2 3.6 + - - -
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Residues in contact with GLU 267 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2632 GLN* 2.9 19.2 + - + +
2642 HIS* 3.1 24.2 + - + +
2662 ARG* 1.3 79.4 - - - +
2682 PHE* 1.3 59.2 + - + +
2692 GLY 3.3 4.7 + - - -
2702 LEU* 3.6 19.7 + - - +
2712 VAL* 5.2 0.7 + - - +
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Residues in contact with PHE 268 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2182 GLN* 2.7 36.6 - - + +
2212 GLN* 2.7 56.1 - - + -
2222 THR* 3.6 3.1 - - - -
2232 ALA 3.0 18.4 - - - -
2242 GLN* 2.9 43.2 - - + +
2302 LEU* 3.5 21.4 - - + +
2642 HIS* 2.9 13.0 + - + +
2652 LEU* 2.6 18.5 - - - +
2672 GLU* 1.3 77.8 - - + +
2692 GLY* 1.3 57.6 + - - +
2722 PHE* 5.6 1.1 - + - -
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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