Contacts of the strand formed by residues 62 - 70 (chain D) in PDB entry 4GUP
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 PHE 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.0 29.8 - - + -
91C THR* 4.7 1.8 - - + -
93C GLN* 3.8 24.5 - - + -
29D GLY 3.0 24.4 + - - -
30D PHE* 3.3 38.1 + + + -
31D HIS* 3.6 24.7 - + - -
32D PRO 3.7 1.3 - - - -
33D SER* 3.4 41.3 - - - -
54D LEU* 4.0 23.3 - - + -
55D SER 3.2 11.9 - - - +
56D PHE* 3.6 17.7 - - + +
60D TRP 3.9 1.8 - - - -
61D SER* 1.3 71.1 - - - +
63D TYR* 1.4 58.2 + - - +
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Residues in contact with TYR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 5.0 4.9 - - - -
30C SER* 5.6 2.8 + - - -
26D TYR* 3.5 27.1 - + - +
27D VAL 3.2 13.0 - - - +
28D SER* 3.8 16.2 - - - -
29D GLY 4.7 0.4 - - - +
30D PHE* 4.1 1.6 - - - -
52D SER* 5.9 1.3 - - - -
53D ASP 4.4 3.5 - - - +
54D LEU* 4.0 1.6 - - - +
55D SER* 3.0 60.1 + - - -
56D PHE 4.2 0.7 - - - -
57D SER* 4.0 28.5 - - - -
61D SER 4.4 2.2 - - - -
62D PHE* 1.4 76.8 - - - +
64D LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D CYS 4.0 0.6 - - - +
26D TYR* 3.3 9.5 - - - -
27D VAL* 2.8 36.1 + - + +
30D PHE* 4.5 5.4 - - + -
35D ILE* 3.9 26.2 - - + -
51D HIS* 3.7 17.3 - - + +
52D SER* 3.4 30.7 - - - +
54D LEU* 3.8 33.9 - - + +
63D TYR* 1.3 75.2 - - - +
65D LEU* 1.3 62.4 + - - +
66D TYR* 3.8 30.1 - - + +
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PRO* 3.7 32.5 - - + +
234C GLY* 4.7 12.8 - - - +
10D TYR* 4.1 9.0 - - - +
24D ASN* 3.6 35.2 - - + +
25D CYS 3.7 13.2 - - - +
26D TYR* 4.0 10.5 - - + +
51D HIS* 3.2 5.0 - - - +
52D SER* 2.7 48.8 + - - +
64D LEU* 1.3 76.0 - - - +
66D TYR* 1.3 68.4 + - - +
67D TYR* 4.2 18.4 - - + -
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Residues in contact with TYR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU 3.7 1.0 - - - +
24D ASN* 3.4 2.4 - - - -
25D CYS* 2.8 49.3 + - + +
27D VAL* 5.1 2.0 - - + -
35D ILE 4.2 13.0 + - - -
37D VAL* 3.7 54.8 + - + +
39D LEU* 4.1 6.1 - - + +
49D VAL* 4.0 22.4 - - + -
50D GLU 3.4 4.3 - - - +
51D HIS* 3.5 34.6 + + + -
64D LEU* 3.8 40.6 - - + +
65D LEU* 1.3 77.1 - - - +
67D TYR* 1.3 58.9 + - - +
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLY* 6.1 3.1 - - - -
12D ARG* 4.3 10.5 - - - +
22D PHE* 3.8 28.7 - + + -
23D LEU 3.2 6.1 - - - +
24D ASN* 3.3 25.4 - - - +
39D LEU* 4.1 2.2 - - - +
50D GLU* 2.9 61.8 + - + +
51D HIS 4.3 13.8 + - - -
52D SER* 4.4 5.4 - - - -
65D LEU* 4.2 20.0 - - + -
66D TYR* 1.3 75.5 - - - +
68D THR* 1.3 67.4 + - - +
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PHE* 3.3 6.2 - - - -
23D LEU* 2.8 33.2 + - - +
39D LEU* 3.5 8.0 - - - +
46D ILE* 3.8 20.4 - - + -
48D LYS* 3.0 29.4 + - + +
49D VAL* 3.3 16.1 - - - +
67D TYR* 1.3 78.1 + - - +
69D GLU* 1.3 75.6 + - - +
70D PHE* 3.6 5.1 + - + +
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D SER* 3.1 19.7 + - - +
21D ASN 3.3 17.5 - - - +
22D PHE* 3.5 33.6 - - + -
68D THR* 1.3 86.1 - - - +
70D PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 4.5 3.6 - - - -
20D SER* 4.6 1.1 - - - -
21D ASN* 2.9 38.4 + - + -
22D PHE 3.3 16.2 - - - -
23D LEU* 3.3 51.8 - - + -
68D THR* 4.2 3.4 - - + +
69D GLU* 1.3 76.3 - - - +
71D THR* 1.3 61.5 + - - +
72D PRO* 3.5 21.7 - - + +
78D TYR* 3.5 49.4 - + + +
95D TRP* 3.9 28.5 - + - -
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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