Contacts of the strand formed by residues 38 - 46 (chain D) in PDB entry 1GXD
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 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ASN* 4.7 0.4 - - - -
34D ASP* 2.4 53.0 + - + +
35D ILE* 4.6 15.6 - - + +
37D GLY* 1.3 81.3 - - - +
39D PRO* 1.3 59.4 - - - +
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Residues in contact with PRO 39 (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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30D ASP* 4.8 10.1 - - - +
32D GLY 3.2 13.5 - - - +
33D ASN* 3.9 15.7 - - - +
34D ASP* 3.5 2.3 - - - +
37D GLY 3.0 13.9 - - - +
38D ASN* 1.3 90.6 - - - +
40D ILE* 1.3 61.3 + - - +
41D LYS* 4.0 25.5 + - - +
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Residues in contact with ILE 40 (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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31D SER* 3.3 24.9 + - - -
32D GLY* 2.8 35.7 + - - +
33D ASN 4.4 0.4 - - - +
34D ASP* 3.5 20.1 + - - +
39D PRO* 1.3 73.6 - - - +
41D LYS* 1.3 77.9 + - - +
42D ARG* 4.9 10.5 - - + -
67D PRO* 5.6 4.7 - - + -
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Residues in contact with LYS 41 (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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28D GLU* 4.5 25.6 - - + +
29D VAL 3.7 9.9 - - - +
30D ASP* 2.9 33.8 + - - +
39D PRO* 4.0 24.4 + - - +
40D ILE* 1.3 82.9 - - - +
42D ARG* 1.3 64.8 + - - +
67D PRO* 3.1 28.3 - - + +
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Residues in contact with ARG 42 (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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28D GLU* 4.5 2.7 - - - -
29D VAL* 2.9 35.7 + - + +
31D SER* 4.5 24.8 + - - -
40D ILE* 4.1 12.2 + - + -
41D LYS* 1.3 77.9 - - - +
43D ILE* 1.3 67.2 + - - +
64D TYR* 2.9 52.6 - - + +
65D THR 3.4 19.1 - - - +
66D ALA* 5.4 1.8 - - - +
67D PRO* 4.8 1.3 - - + -
91D GLU* 4.8 15.8 - - - +
95D LYS* 6.1 0.2 - - - +
97D HIS* 4.5 25.4 - - - +
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Residues in contact with ILE 43 (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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26D GLU* 3.7 35.7 - - + +
27D LYS 4.5 2.0 - - - +
28D GLU* 3.8 35.9 - - + +
42D ARG* 1.3 74.7 - - - +
44D GLN* 1.3 63.6 + - - +
45D TYR* 4.4 5.8 - - + +
64D TYR* 3.2 7.3 - - - -
65D THR* 2.8 47.2 + - + -
66D ALA 3.3 20.4 - - - +
67D PRO* 3.7 16.4 - - + +
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Residues in contact with GLN 44 (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 SER 3.7 0.2 - - - +
26D GLU* 3.4 2.4 - - - -
27D LYS* 2.9 67.0 + - - +
29D VAL* 3.9 18.7 - - + +
43D ILE* 1.3 81.3 - - - +
45D TYR* 1.3 76.0 + - - +
46D GLU* 4.3 2.2 - - - +
62D PHE* 4.1 27.2 - - + -
63D ILE 3.7 4.5 - - - +
64D TYR* 3.7 37.3 + - + -
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Residues in contact with TYR 45 (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 ALA* 4.3 10.1 - - + -
25D SER 3.1 7.4 - - - +
26D GLU* 3.5 37.7 - - + -
43D ILE* 4.4 4.1 - - + +
44D GLN* 1.3 76.0 - - - +
46D GLU* 1.3 59.9 + - - +
47D ILE* 3.1 19.3 + - + -
62D PHE* 3.4 7.1 - - - +
63D ILE* 3.0 51.6 + - + +
65D THR* 3.5 23.3 - - + +
74D VAL 2.1 36.6 + - - -
75D SER* 3.5 4.0 - - - -
76D LEU* 3.6 48.9 - - + -
78D VAL* 5.0 1.1 - - + -
98D ILE* 4.8 3.6 - - + -
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Residues in contact with GLU 46 (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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24D VAL* 3.4 30.7 + - - +
25D SER* 2.7 37.4 + - - -
27D LYS* 5.3 4.2 + - - +
44D GLN* 4.1 6.5 + - - +
45D TYR* 1.3 67.7 - - - +
47D ILE* 1.3 66.7 + - - +
61D GLU* 3.9 11.0 - - + +
62D PHE* 4.0 24.8 - - + -
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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