Contacts of the helix formed by residues 38 - 54 (chain A) in PDB entry 5XOU
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 GLY 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO* 1.3 79.5 - - - +
39A ARG* 1.3 65.7 + - - -
40A GLU 3.2 3.2 + - - -
41A GLU* 3.3 6.9 + - - +
42A VAL* 3.2 17.2 + - - +
86A TYR* 4.9 1.6 + - - -
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Residues in contact with ARG 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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38A GLY* 1.3 69.1 - - - -
40A GLU* 1.3 63.1 + - - +
41A GLU 3.3 1.2 + - - -
42A VAL* 3.3 23.2 + - + +
43A TYR* 4.6 4.7 + - - -
17C T 6.2 2.2 - - - +
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Residues in contact with GLU 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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38A GLY 3.2 0.8 - - - -
39A ARG* 1.3 79.2 - - - +
41A GLU* 1.3 62.2 + - - +
44A PRO* 3.5 18.0 - - - +
4D A 5.6 0.9 + - - -
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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
----------------------------------------------------------
37A PRO* 4.0 15.9 - - + -
38A GLY 3.3 7.3 + - - +
40A GLU* 1.3 82.7 - - - +
42A VAL* 1.4 60.9 + - - +
43A TYR 3.7 0.4 - - - -
44A PRO* 3.5 6.0 - - - +
45A LEU* 2.9 39.5 + - + +
86A TYR* 4.7 9.2 - - + +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.1 0.7 - - + -
37A PRO* 3.7 25.8 - - + +
38A GLY 3.2 10.0 + - - +
39A ARG* 3.3 18.0 + - + +
41A GLU* 1.4 75.7 - - - +
43A TYR* 1.3 74.6 + - + +
45A LEU* 3.0 2.9 + - - +
46A LEU* 2.9 48.5 + - + +
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Residues in contact with TYR 43 (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 ARG 4.6 3.9 + - - -
42A VAL* 1.3 84.6 - - + +
44A PRO* 1.3 73.4 - - + +
46A LEU* 3.4 8.8 + - + +
47A ALA* 3.2 19.6 + - - +
59A ARG* 3.6 42.3 + - - +
61A GLY 4.5 8.5 - - - -
62A ASP* 5.8 1.3 - - - -
17C T 3.7 51.2 + + + +
4D A 4.0 17.3 - - + +
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Residues in contact with PRO 44 (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 ARG 5.4 0.2 - - - +
40A GLU 3.5 25.8 - - - +
41A GLU* 3.5 7.6 - - - +
43A TYR* 1.3 93.0 - - + +
45A LEU* 1.3 63.6 + - + +
47A ALA 3.1 2.4 + - - -
48A GLN* 3.0 19.1 + - - +
4D A 3.1 65.2 + - + +
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Residues in contact with LEU 45 (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 LEU* 4.0 16.4 - - + -
37A PRO* 3.5 23.6 - - + -
41A GLU* 2.9 26.9 + - + +
42A VAL* 3.0 5.0 + - - +
44A PRO* 1.3 76.2 - - + +
46A LEU* 1.3 66.5 + - - +
48A GLN* 3.0 7.7 + - + +
49A VAL* 2.9 26.9 + - - +
79A LEU* 4.7 10.5 - - + -
81A ARG* 3.9 23.6 - - + -
86A TYR* 3.2 45.1 - - + -
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Residues in contact with LEU 46 (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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31A VAL* 4.2 22.7 - - + -
33A LEU* 3.9 25.6 - - + -
42A VAL* 2.9 35.8 + - + +
43A TYR* 3.9 7.4 - - + +
44A PRO 3.3 0.2 - - - -
45A LEU* 1.3 75.3 - - - +
47A ALA* 1.3 63.5 + - - +
49A VAL* 3.1 8.0 + - + +
50A ALA* 2.8 22.7 + - - +
59A ARG* 3.9 26.2 - - + -
62A ASP* 3.4 35.2 - - - +
63A GLY* 4.3 2.0 - - - +
64A LEU* 4.2 8.9 - - + +
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Residues in contact with ALA 47 (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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43A TYR 3.2 11.1 + - - +
44A PRO 3.1 11.2 + - - +
46A LEU* 1.3 78.0 - - - +
48A GLN* 1.4 62.0 + - - +
50A ALA* 3.0 18.3 + - - +
51A ARG* 3.1 13.5 + - - +
59A ARG* 4.9 10.9 - - + +
115A ARG* 4.6 4.1 + - - +
4D A 3.3 35.4 - - - +
5D C 4.3 11.3 + - - +
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Residues in contact with GLN 48 (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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44A PRO 3.0 12.3 + - - +
45A LEU* 3.0 12.3 + - + +
47A ALA* 1.4 74.6 - - - +
49A VAL* 1.3 63.9 + - - +
51A ARG* 3.1 29.5 + - - +
52A ARG* 2.9 24.1 + - - +
79A LEU* 3.7 17.3 - - + -
4D A 4.3 9.6 + - - +
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Residues in contact with VAL 49 (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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31A VAL* 4.3 7.9 - - + -
33A LEU* 4.0 20.9 - - + -
45A LEU 2.9 19.4 + - - +
46A LEU* 3.4 10.8 - - - +
48A GLN* 1.3 75.8 - - - +
50A ALA* 1.3 63.3 + - - +
52A ARG* 3.1 3.1 + - - +
53A ALA* 2.9 22.7 + - - +
64A LEU* 3.9 10.1 - - + -
79A LEU* 3.5 28.2 - - + +
88A TYR* 4.2 13.8 - - + -
90A LEU* 3.7 31.2 - - + -
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Residues in contact with ALA 50 (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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46A LEU 2.8 12.9 + - - +
47A ALA* 3.0 13.0 + - - +
49A VAL* 1.3 76.8 - - - +
51A ARG* 1.3 65.3 + - - +
53A ALA* 3.5 8.7 + - - +
54A GLY 3.8 6.1 + - - +
57A THR* 3.7 18.3 - - - +
58A VAL* 4.0 16.8 - - - +
59A ARG 4.2 1.1 - - - +
64A LEU* 4.2 16.1 - - + +
115A ARG* 3.6 23.1 + - - +
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Residues in contact with ARG 51 (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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47A ALA 3.1 10.6 + - - +
48A GLN* 3.1 26.8 + - - +
50A ALA* 1.3 80.2 - - - +
52A ARG* 1.3 62.6 + - - +
54A GLY* 2.9 17.0 + - - -
115A ARG* 3.3 19.3 - - - +
119A GLU* 6.0 1.8 - - - +
4D A 4.3 13.9 + - - -
5D C 3.9 29.3 + - - +
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Residues in contact with ARG 52 (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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48A GLN 2.9 19.2 + - - +
49A VAL* 4.0 3.4 - - - +
51A ARG* 1.3 76.4 - - - +
53A ALA* 1.3 50.8 + - - +
54A GLY* 3.2 1.0 + - - -
74A VAL* 2.8 27.3 - - - +
78A THR 3.1 27.3 + - - +
79A LEU* 4.3 9.3 - - + +
88A TYR* 4.0 19.5 - - + +
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Residues in contact with ALA 53 (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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49A VAL* 2.9 16.3 + - + +
50A ALA* 3.8 8.3 - - - +
51A ARG 3.2 0.4 - - - -
52A ARG* 1.3 75.0 - - - +
54A GLY* 1.3 63.2 + - - +
55A GLY 4.2 0.2 + - - -
57A THR* 4.8 2.2 - - - +
64A LEU* 5.0 2.0 - - + -
72A VAL 4.6 0.7 - - - +
73A LEU* 3.4 19.7 - - + +
74A VAL* 3.0 37.6 + - - +
88A TYR* 4.3 1.6 + - - +
90A LEU* 3.7 27.8 - - + -
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Residues in contact with GLY 54 (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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50A ALA 3.8 2.2 + - - +
51A ARG 2.9 16.7 + - - -
52A ARG 3.1 1.9 - - - -
53A ALA* 1.3 81.4 - - - +
55A GLY* 1.3 68.7 + - - +
57A THR* 3.0 21.5 + - - -
73A LEU* 3.1 5.6 - - - +
119A GLU* 6.1 0.2 - - - -
122A ARG* 6.0 2.7 - - - -
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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