Contacts of the strand formed by residues 33 - 42 (chain A) in PDB entry 2H41
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 VAL 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 4.5 1.3 - - - -
30A SER* 2.7 29.9 + - - +
31A ASP* 4.1 8.1 - - - +
32A THR* 1.3 81.5 + - - +
34A SER* 1.3 54.7 + - - +
35A GLY 2.7 36.6 - - - +
36A PHE* 3.7 28.5 - - + -
56A SER* 2.7 34.7 + - - +
78A GLN* 3.8 13.0 - - + +
79A ILE 3.0 15.9 - - - +
80A SER* 4.2 1.6 - - - +
81A GLU* 5.3 0.4 - - - +
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 1.3 67.1 - - - +
35A GLY* 1.3 54.7 + - - -
55A PRO* 4.6 1.9 - - - +
56A SER* 3.5 16.6 + - - -
79A ILE* 2.3 30.1 + - - -
80A SER 4.0 5.6 - - - -
81A GLU* 3.1 36.2 - - - +
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 2.7 12.2 - - - +
34A SER* 1.3 81.8 - - - +
36A PHE* 1.3 58.3 + - - -
54A LEU 3.1 11.9 - - - -
55A PRO* 4.1 0.4 - - - -
56A SER* 3.4 9.2 - - - -
79A ILE* 2.7 40.8 + - - +
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.6 31.6 - + + -
28A SER* 3.6 30.1 - - - -
33A VAL* 3.7 11.4 - - + -
35A GLY* 1.3 74.1 - - - -
37A ARG* 1.3 60.8 + - - +
38A VAL 4.3 0.2 - - - -
52A LEU 3.5 0.6 - - - +
53A ASP* 3.2 5.7 - - - +
54A LEU* 2.5 50.1 + - + +
55A PRO 3.1 15.0 - - - -
56A SER* 3.3 25.4 - - - -
58A ALA 3.1 26.9 - - - -
76A VAL* 4.5 1.3 - - + -
77A TYR 3.5 4.3 - - - -
78A GLN* 3.4 31.2 - - + -
79A ILE* 4.5 3.7 - - - +
88A ILE* 3.8 13.2 - - + -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 1.3 75.1 - - - +
38A VAL* 1.3 65.4 + - - +
39A GLU* 4.8 4.8 + - - -
51A TYR* 3.7 50.0 - - + +
52A LEU 3.2 3.4 - - - +
53A ASP* 3.3 22.2 - - - +
76A VAL* 3.7 1.0 - - - -
77A TYR* 2.7 56.6 + - - +
79A ILE* 4.2 8.7 - - + -
85A GLN* 2.5 44.3 + - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 6.4 0.2 - - + -
26A TRP* 3.5 33.7 - - + -
37A ARG* 1.3 78.1 - - - +
39A GLU* 1.3 65.3 + - - +
40A TYR* 4.7 1.8 - - + -
50A GLN 3.4 0.5 - - - +
51A TYR* 3.1 6.9 - - - -
52A LEU* 2.7 48.2 + - + +
54A LEU* 3.8 11.7 - - + -
61A VAL* 3.8 13.7 - - + -
63A ILE* 3.9 26.9 - - + -
74A VAL* 4.0 16.8 - - + -
75A ASN 3.7 3.4 - - - +
76A VAL* 4.3 7.9 - - + -
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 4.8 2.3 + - - -
38A VAL* 1.3 75.6 - - - +
40A TYR* 1.3 65.5 + - - +
41A GLU* 3.7 10.0 - - - +
49A PRO* 3.0 25.6 - - + +
50A GLN 3.1 6.5 - - - +
51A TYR* 3.0 39.2 + - + -
73A ILE 3.3 3.5 - - - +
74A VAL* 3.4 2.1 - - - +
75A ASN* 3.0 46.4 + - + +
77A TYR* 3.8 26.1 + - + -
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 6.4 0.4 - - + -
38A VAL* 4.5 1.3 - - + -
39A GLU* 1.3 79.4 - - - +
41A GLU* 1.3 62.5 + - - +
49A PRO* 4.7 0.4 - - - -
50A GLN* 2.6 82.0 + - + +
52A LEU* 3.6 28.5 - - + +
63A ILE* 3.5 47.4 - - + +
64A PRO* 4.8 5.9 + - - +
65A ASP 6.0 0.4 - - - -
66A LEU* 4.2 17.0 - - + -
72A TYR* 4.5 11.7 - + + -
73A ILE 3.0 9.6 - - - +
74A VAL* 4.2 7.9 - - + -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 3.7 7.9 - - - +
40A TYR* 1.3 76.5 - - - +
42A LEU* 1.3 70.0 + - - +
46A GLY* 5.2 5.0 - - - -
47A ASP* 4.6 10.3 - - - +
48A GLU 4.6 1.6 - - - +
49A PRO* 3.6 35.0 - - + +
50A GLN* 4.9 4.0 - - - +
72A TYR* 3.1 10.3 - - - -
73A ILE* 2.8 49.9 + - + +
75A ASN* 6.1 2.5 - - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU* 1.3 78.2 - - - +
43A SER* 1.3 59.2 + - - +
44A GLU* 3.0 3.6 - - + +
45A GLU* 2.3 42.6 - - + +
46A GLY* 3.1 34.8 + - - +
47A ASP* 4.2 21.8 - - + +
67A LEU* 4.2 7.4 - - + -
70A ARG* 3.6 18.2 - - + +
71A LYS 3.3 8.1 - - - +
72A TYR* 2.8 53.1 - - + +
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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