Contacts of the strand formed by residues 266 - 275 (chain 6) in PDB entry 3J7Y
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 HIS 266 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2226 ASP* 2.6 25.4 + - - +
2246 HIS* 3.1 42.5 + + + +
2596 PRO* 3.0 29.4 - - + +
2606 ALA 4.4 0.7 - - - -
2636 SER* 2.7 29.9 + - - -
2646 GLY 4.4 1.8 - - - -
2656 ILE* 1.3 82.7 - - - +
2676 ARG* 1.3 61.0 - - - +
2686 LEU* 4.0 6.7 - - + -
3196 PHE 3.8 0.2 - - - +
3206 GLN* 3.1 6.4 - - - -
3216 CYS* 2.8 44.7 + - + +
47P PHE* 3.7 17.7 - + - -
49P ASN* 5.3 0.7 - - - -
51P ASN* 5.1 0.2 - - - -
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Residues in contact with ARG 267 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1556 TYR* 2.9 34.0 + - + -
1566 GLY* 3.3 16.0 + - - -
1576 LEU* 4.8 3.6 - - + +
1596 ARG* 5.6 1.4 - - - +
1606 ASP* 3.1 22.6 + - - +
2206 SER* 4.8 0.2 - - - -
2216 LEU* 3.1 60.1 + - + +
2226 ASP* 3.4 19.5 + - - +
2666 HIS* 1.3 73.8 - - - +
2686 LEU* 1.3 65.6 + - - +
3186 PHE* 5.5 5.2 - - + -
3196 PHE 3.6 6.5 - - - +
3206 GLN* 4.6 5.4 - - + +
50P ARG* 3.3 35.3 + - - +
51P ASN* 3.3 29.6 - - + +
52P PRO* 5.1 0.2 - - - +
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Residues in contact with LEU 268 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1776 TYR* 5.8 0.7 - - - +
2186 LEU* 3.8 21.8 - - + -
2196 THR 3.4 3.6 - - - -
2206 SER* 3.2 33.9 - - - +
2246 HIS* 5.4 1.3 - - + -
2346 HIS* 4.3 15.5 - - + +
2546 TYR* 5.9 0.4 - - + +
2576 PRO* 3.9 18.6 - - + -
2666 HIS* 5.2 6.3 - - + -
2676 ARG* 1.3 76.3 - - - +
2696 ALA* 1.3 58.1 + - - +
2706 PHE* 5.9 0.4 - - - -
3186 PHE* 3.2 6.9 - - - +
3196 PHE* 2.8 67.4 + - + +
3216 CYS* 3.7 20.0 - - + -
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Residues in contact with ALA 269 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576 LEU* 3.6 18.4 - - + -
1616 LEU* 4.3 2.2 - - + -
2186 LEU* 3.2 5.9 - - - -
2196 THR* 2.8 39.6 + - - +
2216 LEU* 3.4 22.2 - - + -
2686 LEU* 1.3 77.4 - - - +
2706 PHE* 1.3 62.3 + - - +
2716 LEU* 3.9 17.5 + - + +
3166 LEU* 6.0 0.4 - - + -
3176 SER 3.7 5.8 - - - +
3186 PHE* 4.2 0.9 - - + +
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Residues in contact with PHE 270 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1736 LEU* 4.2 11.2 - - + -
1756 VAL* 3.6 36.8 - - + -
1776 TYR* 4.0 15.3 - + - -
1876 VAL* 3.8 22.7 - - + -
2026 PRO* 4.2 6.3 - - + -
2046 VAL* 5.3 0.7 - - + -
2166 LEU* 3.8 24.0 - - + -
2176 LEU 3.2 6.3 - - - +
2186 LEU* 3.4 35.9 - - + +
2356 TRP* 4.7 3.1 - + - -
2696 ALA* 1.3 73.0 - - - +
2716 LEU* 1.3 67.7 + - - +
3166 LEU* 3.6 5.6 - - - +
3176 SER* 2.8 52.9 + - - +
3196 PHE* 4.8 9.9 - + + -
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Residues in contact with LEU 271 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1616 LEU* 3.4 35.4 - - + -
1626 PHE* 4.7 9.0 - - + -
1736 LEU* 4.8 1.1 - - - -
2156 THR 3.5 2.1 - - - +
2166 LEU* 3.3 7.4 - - - +
2176 LEU* 2.8 64.8 + - + +
2196 THR* 4.4 0.9 - - - +
2696 ALA* 4.1 10.8 - - + +
2706 PHE* 1.3 86.0 - - - +
2726 LEU* 1.3 61.9 + - - +
2736 PHE* 4.1 24.2 - - + -
3006 THR* 4.3 15.5 - - + -
3036 PHE* 6.4 0.2 - - + -
3136 PRO* 6.1 1.3 - - + -
3156 GLY 3.6 4.5 - - - -
3166 LEU* 3.5 15.9 - - + -
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Residues in contact with LEU 272 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716 VAL* 5.3 8.1 - - + -
1736 LEU* 3.9 14.6 - - + -
2066 TYR* 3.8 24.5 - - + -
2146 TRP* 3.5 40.4 - - + -
2156 THR 3.7 2.0 - - - -
2166 LEU* 3.7 39.9 - - + +
2406 ILE* 5.7 0.2 - - + -
2716 LEU* 1.3 73.8 - - - +
2736 PHE* 1.3 61.9 + - - +
3136 PRO* 3.4 6.1 - - - +
3146 ALA* 2.8 27.4 + - + -
3156 GLY* 2.8 30.8 + - - +
3166 LEU* 5.0 0.2 - - - +
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Residues in contact with PHE 273 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1626 PHE* 5.0 4.3 - + - -
2146 TRP* 3.2 34.5 - - - -
2156 THR* 3.2 30.0 + - - +
2176 LEU* 4.6 12.3 - - + -
2716 LEU* 4.1 35.0 - - + -
2726 LEU* 1.3 76.0 - - - +
2746 LYS* 1.3 60.5 + - - +
3036 PHE* 4.4 10.1 - + - -
3046 TYR* 3.7 28.3 - + - -
3086 GLN* 3.7 24.9 - - - -
3116 MET* 3.4 17.5 - - + -
3126 THR* 3.3 10.8 - - - +
3136 PRO* 3.6 28.3 - - + -
3146 ALA 4.0 0.7 - - - +
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Residues in contact with LYS 274 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1706 ARG* 5.1 13.2 - - - +
1716 VAL* 5.4 3.4 - - + -
2146 TRP* 3.9 19.3 - - + -
2736 PHE* 1.3 70.8 - - - +
2756 GLN* 1.3 61.8 + - - +
2766 ASP* 3.8 2.2 + - - +
3106 THR 4.2 0.2 - - - +
3116 MET* 3.1 27.2 - - - +
3126 THR* 2.8 37.0 + - - +
3136 PRO 5.0 1.8 - - - -
3146 ALA* 3.5 30.5 - - + +
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Residues in contact with GLN 275 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136 LEU* 2.8 58.8 + - + +
2146 TRP 3.5 5.5 - - - +
2156 THR* 3.1 27.8 - - + +
2396 ASN* 3.0 40.8 + - - +
2736 PHE 3.8 0.2 + - - -
2746 LYS* 1.3 71.0 - - - +
2766 ASP* 1.3 65.6 + - - +
2776 GLN 3.9 15.0 + - - +
2786 PRO* 4.9 3.6 - - - -
2796 ILE* 4.5 2.8 - - - +
2816 PHE* 4.1 7.5 - - - -
3116 MET* 3.7 25.2 - - + +
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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