Contacts of the helix formed by residues 256 - 264 (chain 4) 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 ASP 256 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2544 THR* 3.1 1.0 - - - +
2554 GLU* 1.3 76.9 - - - +
2574 LEU* 1.3 52.1 + - - +
2584 TYR 3.1 2.2 - - - -
2594 HIS* 2.8 22.0 + - - +
2604 GLN* 2.6 67.4 + - - +
1357 LYS* 4.5 11.1 + - - +
1367 ASP 5.8 1.0 + - - -
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Residues in contact with LEU 257 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1854 VAL* 4.4 0.2 - - + -
1904 CYS* 3.8 37.7 - - + +
1944 PHE* 5.0 4.9 - - + -
2484 LEU* 3.6 15.7 - - + +
2544 THR* 3.2 38.0 + - + +
2564 ASP* 1.3 75.6 + - - +
2584 TYR* 1.3 59.8 + - - +
2604 GLN* 3.3 31.4 - - + +
2614 LEU* 2.9 30.3 + - - +
2684 VAL* 4.2 26.9 - - + -
2724 MET* 5.6 3.4 - - + -
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Residues in contact with TYR 258 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2454 ALA* 4.4 3.8 - - + -
2464 ARG* 3.3 18.8 - - + +
2474 ASN* 3.6 21.1 - - + -
2484 LEU* 3.4 29.9 - - + +
2494 LEU* 3.1 48.0 - - + +
2544 THR 3.1 4.9 + - - -
2554 GLU 3.7 12.3 - - - +
2574 LEU* 1.3 76.6 - - - +
2594 HIS* 1.3 71.6 + + - +
2614 LEU* 3.9 9.3 + - + +
2624 LEU* 3.5 22.5 + - + +
3074 ASN 3.8 1.6 + - - -
3084 VAL* 3.1 46.2 - - + +
3094 GLY 4.5 2.7 + - - -
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Residues in contact with HIS 259 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2494 LEU* 5.6 9.1 - - + +
2554 GLU* 2.9 29.5 + - + -
2564 ASP* 2.8 22.4 + - - +
2584 TYR* 1.3 87.6 - + - +
2604 GLN* 1.3 54.6 + - - +
2614 LEU 3.1 2.2 - - - -
2624 LEU* 3.0 16.8 + - + +
2634 ASN* 2.7 45.0 + - - +
1357 LYS* 5.1 0.4 - - - +
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Residues in contact with GLN 260 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1844 ASN* 5.5 3.0 + - - -
1854 VAL* 3.3 42.4 - - + +
1864 SER 5.2 0.6 + - - +
1904 CYS* 4.1 4.2 - - - -
2564 ASP* 2.6 39.5 + - - +
2574 LEU* 2.9 27.3 + - + +
2594 HIS* 1.3 72.5 - - - +
2614 LEU* 1.3 57.0 + - - +
2634 ASN* 3.6 7.5 - - - +
2644 TYR* 3.0 26.0 + - - -
2684 VAL* 3.6 9.3 - - + +
1357 LYS* 3.2 19.0 - - - +
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Residues in contact with LEU 261 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2484 LEU* 5.9 1.1 - - + -
2574 LEU* 2.9 12.2 + - + +
2584 TYR* 4.1 9.9 - - + +
2604 GLN* 1.3 74.1 - - - +
2624 LEU* 1.3 64.9 + - - +
2634 ASN 3.1 0.9 - - - -
2654 PRO* 2.9 37.4 - - + +
2684 VAL* 3.5 41.0 - - + +
2694 ILE* 4.2 19.5 - - + -
2724 MET* 4.5 17.7 - - + -
3054 PRO* 4.3 16.6 - - + -
3084 VAL* 4.7 11.0 - - + -
3254 LEU* 3.6 26.7 - - + -
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Residues in contact with LEU 262 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2584 TYR* 3.5 17.8 + - + +
2594 HIS* 3.0 21.4 + - + +
2614 LEU* 1.3 81.8 - - + +
2634 ASN* 1.3 64.3 + - - +
2654 PRO* 3.7 1.2 - - - +
3084 VAL* 3.7 43.7 - - + +
3094 GLY* 5.4 2.5 - - - +
3234 ASP 3.4 3.5 - - - +
3244 LYS* 3.0 42.4 - - + +
3254 LEU* 3.7 27.6 - - + +
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Residues in contact with ASN 263 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2594 HIS* 2.7 27.6 + - - +
2604 GLN 3.8 1.8 - - - +
2624 LEU* 1.3 80.3 - - - +
2644 TYR* 1.3 90.3 + - + +
2654 PRO* 3.6 1.6 - - - +
3234 ASP* 3.4 20.9 - - - +
3244 LYS* 4.6 9.6 - - - +
1357 LYS* 2.7 34.0 + - - +
1367 ASP 4.5 8.4 + - - +
1387 VAL* 3.6 28.3 - - + +
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Residues in contact with TYR 264 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1824 GLY 3.4 2.1 + - - -
1834 THR* 3.2 61.5 - - + +
1854 VAL* 4.6 1.3 - - + -
2604 GLN 3.0 14.4 + - - +
2614 LEU 3.4 2.9 - - - -
2634 ASN* 1.3 86.8 - - + +
2654 PRO* 1.3 64.7 - - - +
2664 GLN* 3.3 3.4 - - + -
2674 GLU* 3.3 13.6 + - + +
2684 VAL* 3.3 15.4 + - - +
3234 ASP* 5.4 6.3 - - + -
1357 LYS* 3.4 26.4 - - - +
1387 VAL* 3.5 19.9 - - + +
1397 LEU 3.4 12.3 + - - -
1417 VAL* 3.2 27.0 - - - +
1427 ILE* 4.1 18.2 - - + +
3037 ARG* 4.2 8.3 - - + +
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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