Contacts of the helix formed by residues 42 - 55 (chain A) in PDB entry 4XIH
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 THR 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 2.7 48.4 + - + +
40A ALA 4.0 2.0 - - - +
41A PHE* 1.3 82.3 + - - +
43A GLY* 1.3 58.7 + - - +
44A ILE* 4.0 9.7 - - - +
45A CYS* 3.1 17.0 + - - +
46A GLN* 2.9 29.5 + - - +
80A TRP* 4.7 0.2 - - - -
83B GLN 4.9 0.7 - - - -
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Residues in contact with GLY 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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41A PHE 4.2 0.8 + - - -
42A THR* 1.3 72.4 - - - +
44A ILE* 1.3 56.2 + - - +
46A GLN* 3.2 3.0 + - - +
47A GLY 2.9 25.8 + - - -
53B ARG* 3.4 16.7 + - - -
82B THR 5.5 0.2 + - - -
83B GLN 3.2 21.7 + - - -
84B SER* 3.3 23.9 - - - +
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Residues in contact with ILE 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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38A PRO* 4.7 9.0 - - + -
42A THR* 4.0 9.0 - - - +
43A GLY* 1.3 76.5 - - - +
45A CYS* 1.3 79.1 + - - +
47A GLY* 3.6 1.2 + - - -
48A GLU* 3.4 20.1 + - - +
133A LYS* 3.5 38.1 - - + +
136A GLY 6.1 0.2 - - - +
138A VAL* 4.9 4.0 - - + -
53B ARG* 5.4 0.2 - - - +
82B THR 5.3 2.8 + - - +
83B GLN 4.7 0.2 + - - -
85B GLY* 3.7 31.6 - - - +
87B THR* 4.4 10.8 - - + -
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Residues in contact with CYS 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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37A PHE* 3.9 15.3 - - + -
38A PRO* 3.4 30.3 - - - -
39A LEU 3.2 37.9 - - - +
42A THR* 3.1 20.1 + - - +
43A GLY 3.3 0.2 - - - -
44A ILE* 1.3 81.8 - - - +
46A GLN* 1.3 66.6 + - - +
47A GLY 3.3 0.2 - - - -
48A GLU* 3.4 7.7 + - - +
49A LEU* 3.0 30.1 + - - +
80A TRP* 4.1 5.6 - - + -
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Residues in contact with GLN 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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41A PHE* 5.0 2.6 - - - -
42A THR 2.9 17.7 + - - +
43A GLY* 3.4 9.2 - - - +
45A CYS* 1.3 77.1 - - - +
47A GLY* 1.3 56.4 + - - +
49A LEU* 5.1 0.2 - - - -
50A ASP* 2.8 62.9 + - - +
53A ARG* 5.1 0.6 - - - +
80A TRP* 2.7 32.0 + - - -
84A SER* 2.7 27.7 + - - +
86A PHE* 3.7 3.4 - - - -
53B ARG* 3.6 20.2 - - - +
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Residues in contact with GLY 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 GLY 2.9 11.4 + - - -
44A ILE 3.6 2.0 + - - -
46A GLN* 1.3 76.9 - - - +
48A GLU* 1.3 61.0 + - - +
50A ASP* 3.8 1.9 - - - +
51A GLN* 3.1 25.6 + - - +
138A VAL* 6.3 2.0 - - - -
53B ARG* 3.4 21.0 - - - +
54B ASP* 3.2 25.3 - - - +
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Residues in contact with GLU 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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35A VAL* 3.6 14.9 - - + +
37A PHE* 3.7 20.1 - - - +
38A PRO* 5.0 1.0 - - - +
44A ILE 3.4 13.5 + - - +
45A CYS* 3.7 8.9 - - - +
46A GLN 3.2 0.2 - - - -
47A GLY* 1.3 76.8 - - - +
49A LEU* 1.3 66.5 + - + +
51A GLN* 3.2 4.5 + - - +
52A LEU* 3.1 11.6 + - - +
116A ALA* 4.4 4.8 - - - +
133A LYS* 5.4 6.8 - - - +
138A VAL* 6.3 2.0 - - - -
139A ARG* 2.1 55.5 + - + +
141A GLN* 2.8 36.8 + - - +
144A TRP* 3.9 2.6 - - - -
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Residues in contact with LEU 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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35A VAL* 4.1 25.8 - - + -
37A PHE* 4.0 23.3 - - + -
45A CYS 3.0 18.4 + - - +
48A GLU* 1.3 79.0 - - + +
50A ASP* 1.3 55.9 + - - +
52A LEU* 3.2 15.5 + - + +
53A ARG* 2.7 34.1 + - - +
68A ALA* 4.2 12.3 - - + -
80A TRP* 3.3 32.1 - - + -
86A PHE* 3.5 26.4 - - + -
88A PHE* 4.0 9.9 - - + -
90A LEU* 4.4 7.2 - - + -
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Residues in contact with ASP 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 GLN* 2.8 58.7 + - - +
47A GLY 3.8 0.2 - - - +
49A LEU* 1.3 72.3 - - - +
51A GLN* 1.3 56.6 + - - +
53A ARG* 3.2 26.8 + - - +
54A ASP* 2.7 41.7 + - - -
86A PHE* 3.5 9.7 - - - -
53B ARG* 3.7 2.9 + - - -
54B ASP* 2.7 37.9 - - + +
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Residues in contact with GLN 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 GLY 3.1 16.0 + - - +
48A GLU* 3.4 11.2 - - - +
50A ASP* 1.3 77.1 - - - +
52A LEU* 1.3 61.8 + - - +
54A ASP* 3.5 4.7 + - - -
55A HIS* 3.2 41.5 + - + +
138A VAL* 4.3 9.7 - - - +
139A ARG 3.5 14.2 + - - +
141A GLN* 3.2 46.7 + - + +
142A ARG* 5.1 1.0 + - - +
53B ARG 4.7 1.6 + - - -
54B ASP 3.5 26.2 + - - +
55B HIS* 5.5 0.2 - - - -
57B PRO* 3.5 23.4 - - - +
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Residues in contact with LEU 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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33A LEU* 4.1 13.5 - - + -
35A VAL* 4.4 15.9 - - + -
48A GLU* 3.1 10.5 + - + +
49A LEU* 3.4 20.6 - - + +
51A GLN* 1.3 77.0 - - - +
53A ARG* 1.3 62.7 + - - +
55A HIS 3.3 4.0 + - - -
56A LEU* 3.0 26.4 + - + +
59A PHE* 3.5 38.6 - - + -
66A ALA* 4.4 10.8 - - + -
67A LEU 5.9 0.2 - - - -
68A ALA* 4.9 3.6 - - + +
88A PHE* 3.8 37.9 - - + -
141A GLN* 3.1 14.4 + - - +
144A TRP* 4.7 2.5 - - + -
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Residues in contact with ARG 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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46A GLN* 5.1 0.2 - - - +
49A LEU 2.7 20.5 + - - +
50A ASP* 3.4 37.1 + - - +
52A LEU* 1.3 73.2 - - - +
54A ASP* 1.3 84.3 + - - +
55A HIS 3.2 0.7 + - - -
56A LEU* 3.3 20.0 + - + +
57A PRO* 4.9 1.0 - - - +
84A SER* 2.6 41.2 + - - +
85A GLY* 3.6 20.6 - - - +
86A PHE* 4.0 11.0 - - + -
87A THR 5.8 0.4 - - - +
88A PHE* 4.0 11.0 - - + -
54B ASP* 4.1 4.6 + - - -
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Residues in contact with ASP 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 ASP 2.7 27.1 + - - +
51A GLN* 3.9 7.0 + - - +
52A LEU 3.3 0.2 - - - -
53A ARG* 1.3 99.6 + - - +
55A HIS* 1.3 72.9 + - + +
56A LEU 3.6 0.2 - - - -
57A PRO* 5.0 2.7 - - - +
54B ASP* 4.2 6.8 - - - +
55B HIS* 3.6 29.7 + - + +
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Residues in contact with HIS 55 (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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51A GLN* 3.2 37.3 + - + +
52A LEU 3.3 5.8 + - - -
53A ARG 3.2 0.6 - - - -
54A ASP* 1.3 89.2 + - + +
56A LEU* 1.3 64.3 + - - +
57A PRO* 3.4 6.1 - - - -
58A GLU* 3.2 34.8 + - - +
59A PHE* 3.2 25.9 - - + -
141A GLN* 5.2 3.6 - - + -
142A ARG* 6.3 3.8 - - + +
145A THR* 5.8 1.3 - - + -
55B HIS* 5.1 7.7 - + - -
58B GLU* 4.2 18.3 + - - -
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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