Contacts of the helix formed by residues 45 - 55 (chain B) in PDB entry 1X7O
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B MSE 1.3 73.2 - - - +
46B VAL* 1.3 66.6 + - - -
47B ARG 3.2 2.7 - - - -
48B PRO* 3.5 7.2 - - - +
49B ILE* 3.1 31.5 + - - +
104B PRO* 5.2 2.2 - - - +
105B GLU 6.2 0.7 - - - -
106B VAL* 3.4 15.3 + - - -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLY* 1.3 72.4 - - - +
47B ARG* 1.3 62.0 + - + +
49B ILE* 4.8 0.9 - - - -
50B SER* 2.8 34.3 + - - -
71B SER* 4.3 0.9 - - - +
73B TRP* 3.5 42.0 - - + -
74B ALA* 3.8 30.1 - - + +
77B LEU* 3.7 11.0 - - + +
105B GLU* 3.7 25.1 - - + +
106B VAL* 4.2 10.5 - - + +
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A SER 5.4 0.2 + - - -
258A ALA* 3.2 39.8 + - - +
259A SER* 5.5 3.0 - - - +
46B VAL* 1.3 81.3 - - + +
48B PRO* 1.3 74.4 - - + +
50B SER* 3.1 4.9 + - - -
51B LEU* 3.0 44.9 + - + +
73B TRP* 3.8 34.4 - - + -
174B THR* 4.0 21.1 + - - +
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Residues in contact with PRO 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 3.9 11.7 - - + -
44B MSE 3.4 18.8 - - - +
45B GLY* 3.5 14.1 - - - +
47B ARG* 1.3 96.0 - - + +
49B ILE* 1.3 60.5 + - - +
51B LEU* 3.2 3.6 + - + -
52B ALA 3.0 17.3 + - - -
170B VAL* 6.2 1.1 - - + -
174B THR* 4.8 6.1 - - + +
175B GLY* 4.1 31.2 - - - +
178B PHE* 3.3 14.5 - - + -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 3.9 18.2 - - + +
45B GLY 3.1 22.9 + - - +
46B VAL* 3.8 3.6 - - - +
48B PRO* 1.3 75.3 - - - +
50B SER* 1.3 63.3 + - - +
52B ALA* 3.2 9.8 + - + +
53B VAL* 3.1 27.8 + - + +
59B VAL* 5.1 3.6 - - + -
62B LEU* 4.2 15.3 - - + -
77B LEU* 4.2 20.0 - - + -
81B VAL* 5.8 0.4 - - + -
106B VAL* 3.5 32.5 - - + -
107B VAL 4.1 1.8 - - - +
108B ALA* 3.7 33.7 - - + +
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL 2.8 22.4 + - - -
47B ARG 3.1 5.8 + - - -
49B ILE* 1.3 76.9 - - - +
51B LEU* 1.3 58.8 + - - +
53B VAL* 3.5 6.6 + - - +
54B GLU* 2.9 33.8 + - - +
73B TRP* 2.9 29.6 + - - -
77B LEU* 3.8 14.7 - - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ALA* 5.0 16.4 - - + -
47B ARG* 3.0 43.9 + - + +
48B PRO* 3.2 8.7 + - + +
50B SER* 1.3 74.0 - - - +
52B ALA* 1.3 65.7 + - - +
54B GLU* 3.4 24.6 + - - +
55B HIS* 3.1 41.0 + - + +
174B THR 4.4 0.4 - - - +
175B GLY* 3.6 38.8 - - - +
176B SER* 5.4 0.4 - - - -
178B PHE* 3.8 4.7 - - + +
179B SER* 5.8 3.4 - - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO 3.0 12.4 + - - +
49B ILE* 3.2 13.9 + - + +
51B LEU* 1.3 76.2 - - - +
53B VAL* 1.3 60.8 + - + +
55B HIS 3.4 0.2 + - - -
56B GLY 3.3 4.7 + - - -
57B TRP* 3.0 39.1 + - + +
59B VAL* 5.0 2.7 - - + -
110B VAL* 4.7 12.6 - - + -
178B PHE* 3.7 35.8 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.1 22.2 + - + +
50B SER* 3.8 7.2 - - - +
52B ALA* 1.3 73.0 - - - +
54B GLU* 1.3 67.0 + - - +
55B HIS 3.3 0.7 + - - -
56B GLY* 3.4 11.3 + - - -
57B TRP 4.5 6.3 - - - -
59B VAL* 3.8 22.7 - - + -
77B LEU* 4.7 2.2 - - + -
80B THR* 5.6 6.3 - - + -
81B VAL* 3.9 31.6 - - + -
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B SER* 2.9 20.4 + - - +
51B LEU* 3.7 21.1 - - - +
53B VAL* 1.3 80.9 - - - +
55B HIS* 1.3 77.7 + - + +
56B GLY 3.7 0.5 + - - -
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.1 38.1 + - + +
52B ALA 3.4 0.2 + - - -
53B VAL 3.2 0.2 - - - -
54B GLU* 1.3 100.7 + - + +
56B GLY* 1.3 57.8 + - - +
57B TRP* 3.5 12.7 + - + -
178B PHE 3.4 27.5 + - - +
179B SER* 3.5 28.7 - - - -
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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