Contacts of the strand formed by residues 21 - 30 (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 ASN 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D SER* 3.4 13.0 - - - -
12D ARG 3.5 0.3 + - - -
13D HIS* 3.0 62.5 + - - +
14D PRO 4.1 7.7 + - - -
15D ALA* 5.0 4.1 - - - +
16D GLU* 5.2 3.0 + - - +
19D LYS* 5.2 3.2 + - - +
20D SER* 1.3 78.5 + - - +
22D PHE* 1.4 78.4 + - - +
69D GLU* 3.3 8.0 - - - +
70D PHE* 2.9 40.7 + - + +
72D PRO* 4.4 9.5 - - + +
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Residues in contact with PHE 22 (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* 3.3 5.7 - - - -
12D ARG* 3.0 81.4 + - + +
13D HIS* 5.4 1.8 - - - -
21D ASN* 1.4 92.0 + - - +
23D LEU* 1.4 59.3 + - - +
24D ASN* 3.8 7.3 + - - +
67D TYR* 3.8 24.5 - + + -
68D THR 3.3 9.0 - - - -
69D GLU* 3.5 46.2 - - + -
70D PHE* 3.3 5.3 - - - -
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Residues in contact with LEU 23 (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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9D VAL* 4.0 13.5 - - + -
10D TYR 3.7 10.8 - - - +
22D PHE* 1.4 69.1 - - - +
24D ASN* 1.3 59.8 + - - +
39D LEU* 4.1 25.4 - - + +
40D LEU 4.7 1.6 - - - +
46D ILE* 4.9 6.5 - - + -
66D TYR 3.7 0.7 - - - +
67D TYR* 3.2 4.7 - - - -
68D THR* 2.8 34.4 + - - +
70D PHE* 3.3 25.7 - - + -
78D TYR* 3.8 30.7 - - + -
79D ALA 4.7 7.2 - - - +
95D TRP* 3.7 39.3 - - + -
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Residues in contact with ASN 24 (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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233C SER 3.4 27.2 + - - +
8D GLN 3.8 1.0 - - - +
9D VAL* 3.4 8.9 - - - +
10D TYR* 2.8 66.1 + - + +
12D ARG* 3.4 24.1 + - - +
22D PHE* 4.3 7.2 - - - +
23D LEU* 1.3 74.0 - - - +
25D CYS* 1.4 60.2 + - - +
26D TYR 4.1 0.7 - - - -
39D LEU* 5.0 0.4 - - - -
65D LEU* 3.6 19.2 - - + +
66D TYR 3.4 3.4 - - - -
67D TYR* 3.3 21.0 - - - +
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Residues in contact with CYS 25 (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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7D ILE* 3.8 20.4 - - - -
8D GLN 3.5 2.2 - - - -
9D VAL* 4.0 4.3 - - + -
24D ASN* 1.4 73.6 - - - +
26D TYR* 1.3 59.6 + - - +
27D VAL* 3.6 12.3 + - - +
37D VAL* 4.5 0.7 - - - -
39D LEU* 3.8 14.1 - - + -
64D LEU 4.0 0.2 - - - +
65D LEU* 3.7 2.3 - - - +
66D TYR* 2.8 41.5 + - + +
80D CYS* 2.0 51.8 - - + -
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Residues in contact with TYR 26 (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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229C ASP* 5.4 3.6 - - + -
230C ILE 4.5 6.2 + - - -
231C LEU* 3.7 25.1 - - + -
232C PRO* 3.7 34.1 - - + +
6D LYS 3.2 14.2 - - - +
8D GLN* 3.0 26.8 + - + +
10D TYR* 3.6 25.6 - - + +
24D ASN 4.1 0.2 - - - -
25D CYS* 1.3 70.2 - - - +
27D VAL* 1.3 59.4 + - - +
28D SER* 4.0 18.0 + - - -
63D TYR* 3.5 42.5 - + + +
64D LEU 3.3 18.6 - - - -
65D LEU* 4.0 8.5 - - + -
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Residues in contact with VAL 27 (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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5D PRO* 3.5 29.2 - - + -
6D LYS 3.7 2.5 - - - -
7D ILE* 4.5 8.7 - - + -
25D CYS* 4.3 13.0 - - - +
26D TYR* 1.3 72.2 - - - +
28D SER* 1.4 64.4 + - - +
30D PHE* 3.7 14.4 - - + -
35D ILE* 3.9 13.2 - - + -
37D VAL* 3.8 28.3 - - + -
63D TYR* 3.2 2.6 - - - +
64D LEU* 2.8 42.0 + - + +
66D TYR* 5.1 2.0 - - + -
82D VAL* 4.2 13.9 - - + -
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Residues in contact with SER 28 (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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229C ASP* 4.4 7.4 + - - -
5D PRO* 3.6 1.0 - - - +
6D LYS* 2.8 47.5 + - - +
8D GLN* 4.3 4.9 + - - -
26D TYR* 4.0 22.8 + - - -
27D VAL* 1.4 77.4 - - - +
29D GLY* 1.3 63.8 + - - +
30D PHE* 3.6 3.8 - - - -
62D PHE 3.7 7.2 - - - -
63D TYR* 3.8 13.2 - - - -
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Residues in contact with GLY 29 (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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3D ARG* 3.4 26.1 + - - +
4D THR 3.5 14.4 - - - +
6D LYS* 4.8 0.3 + - - +
28D SER* 1.3 76.5 - - - +
30D PHE* 1.3 58.5 + - - +
61D SER* 3.7 24.1 + - - -
62D PHE 3.0 8.7 + - - -
63D TYR* 4.7 0.4 - - - +
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Residues in contact with PHE 30 (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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3D ARG* 3.4 19.5 - - - +
5D PRO* 3.6 31.0 - - + -
27D VAL* 3.7 27.1 - - + -
28D SER 3.7 5.8 - - - -
29D GLY* 1.3 75.8 - - - +
31D HIS* 1.4 63.0 + - - +
32D PRO 3.2 25.1 - - - -
33D SER 4.0 8.3 - - - -
35D ILE* 3.7 30.3 - - + -
54D LEU* 5.4 0.7 - - + -
61D SER* 3.6 4.5 - - - -
62D PHE* 3.3 61.8 + + + -
63D TYR* 4.1 2.0 - - - -
64D LEU* 4.5 10.1 - - + -
84D HIS* 3.6 12.3 - + - +
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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