Contacts of the strand formed by residues 32 - 39 (chain D) in PDB entry 6H7L
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 32 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 3.2 23.8 - - + +
29D PHE 2.7 23.7 + - - +
30D ALA* 3.7 8.5 + - - +
31D LEU* 1.3 74.7 - - - +
33D ILE* 1.3 65.3 + - - +
34D MET* 4.1 5.8 - - - +
52D HIS* 3.2 7.4 + - - -
53D SER* 2.9 30.3 + - - -
71D ARG* 2.8 40.6 + - - +
76D ASN* 4.8 3.0 + - - -
97D VAL* 4.8 1.6 - - + -
98D LYS 3.2 17.7 - - - +
99D ASP* 4.4 0.7 - - - -
100D PHE* 3.8 6.9 - - - -
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Residues in contact with ILE 33 (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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146B PRO* 3.7 29.6 - - + -
147B PHE* 4.1 14.4 - - + -
150B GLN* 5.4 3.8 - - - +
32D ASN* 1.3 78.9 - - - +
34D MET* 1.3 71.7 + - - +
35D GLY* 4.7 0.9 - - - +
50D ALA* 3.9 19.7 - - + -
51D ILE 3.6 10.5 - - - +
52D HIS* 3.8 15.3 - - + -
96D ASN* 3.7 2.1 - - - +
97D VAL* 3.3 4.9 - - - +
98D LYS* 2.8 58.2 + - + +
100D PHE* 3.9 14.1 - - + -
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Residues in contact with MET 34 (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 CYS* 4.2 7.4 - - - +
24D ALA* 4.0 17.9 - - + -
28D ILE* 5.4 1.6 - - + -
32D ASN* 4.1 3.8 - - - +
33D ILE* 1.3 77.5 - - - +
35D GLY* 1.3 58.1 + - - +
50D ALA* 3.6 0.7 - - - -
51D ILE* 2.8 37.9 + - + +
69D ILE* 3.9 0.7 - - - +
71D ARG* 3.3 39.4 - - - +
76D ASN* 3.8 33.2 - - + +
77D THR 4.3 1.6 - - - -
78D VAL* 3.8 39.5 - - + -
96D ASN 3.4 4.9 - - - +
97D VAL* 4.0 20.2 - - + -
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Residues in contact with GLY 35 (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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33D ILE* 4.2 1.7 - - - +
34D MET* 1.3 76.6 - - - +
36D TRP* 1.3 68.1 + - - -
37D TYR* 4.6 6.7 - - - -
49D ALA 3.3 10.3 - - - -
50D ALA* 4.0 7.0 - - - -
69D ILE* 4.2 2.7 - - - -
78D VAL* 4.8 1.8 - - - +
95D CYS* 3.4 8.5 - - - -
96D ASN* 2.8 36.7 + - - +
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Residues in contact with TRP 36 (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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6D GLU* 3.9 25.6 - - + -
7D SER 5.0 0.9 - - - -
20D LEU* 3.6 43.1 - - + -
21D SER 3.7 6.5 - - - -
22D CYS* 3.6 40.2 - - + -
35D GLY* 1.3 79.6 - - - -
37D TYR* 1.3 61.6 + - - +
47D LEU* 3.7 4.3 - - - +
48D VAL* 2.9 28.2 + - + -
49D ALA 2.7 17.3 + - - +
69D ILE* 3.9 16.8 - - + -
78D VAL* 3.9 14.7 + - + +
79D TYR 4.1 1.0 - - - -
80D LEU* 3.6 42.9 - - + +
93D TYR* 4.2 13.2 - - + -
94D TYR 3.4 19.3 - - - -
95D CYS* 4.0 5.6 - - - -
114D THR* 4.7 2.5 - - + -
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Residues in contact with TYR 37 (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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35D GLY* 4.8 5.6 - - - -
36D TRP* 1.3 77.7 - - - +
38D ARG* 1.3 58.3 + - - +
45D ARG* 3.9 14.8 - - + -
46D GLU 3.3 9.4 - - - +
47D LEU* 3.4 46.3 - - + +
48D VAL* 3.8 3.6 - - - -
93D TYR* 3.3 6.8 - - - +
94D TYR* 2.7 35.3 + - + +
96D ASN* 3.4 29.7 + - + -
98D LYS* 3.7 23.2 + - - -
110D TRP* 3.5 38.6 - + + -
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Residues in contact with ARG 38 (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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37D TYR* 1.3 76.0 - - - +
39D GLN* 1.3 61.6 + - - +
40D ALA 5.2 0.7 - - - +
44D GLN 4.1 0.2 - - - +
45D ARG* 3.3 5.0 - - - -
46D GLU* 2.8 64.7 + - + +
48D VAL* 3.4 21.2 - - + +
62D SER* 3.3 28.1 + - - -
63D VAL* 4.0 13.8 - - - +
67D PHE* 4.3 1.0 - - - -
88D GLU 4.9 4.8 + - - -
89D ASP* 2.9 38.7 + - - +
91D ALA* 4.0 14.6 - - + -
92D VAL 3.3 10.3 - - - +
93D TYR* 3.0 34.4 + - + -
94D TYR* 4.7 0.9 - - - -
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Residues in contact with GLN 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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38D ARG* 1.3 74.6 - - - +
40D ALA* 1.3 63.7 + - - +
41D PRO* 3.9 1.2 - - - +
43D LYS 3.2 27.0 + - - +
44D GLN* 4.3 3.2 - - - +
45D ARG* 4.0 31.4 + - + +
91D ALA* 3.5 3.1 - - - -
92D VAL* 3.0 30.6 + - + +
94D TYR* 4.1 27.7 + - + +
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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