Contacts of the helix formed by residues 39 - 51 (chain A) in PDB entry 3UMO
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 3.9 13.7 - - - -
10A ALA 4.2 9.9 - - - -
12A SER* 4.1 2.6 + - - -
38A GLY* 1.3 73.7 - - - -
40A GLY* 1.3 59.4 + - - +
41A GLY 3.6 1.8 - - - -
42A ILE* 3.4 3.0 + - - -
43A ASN* 2.9 39.5 + - - +
256A ASP* 4.8 0.2 - - - -
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Residues in contact with GLY 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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8A THR* 4.0 2.6 - - - +
10A ALA 5.2 0.4 + - - -
39A GLY* 1.3 69.3 - - - +
41A GLY* 1.3 57.3 + - - +
43A ASN* 3.1 5.0 + - - +
44A VAL* 2.9 30.0 + - - +
137A SER* 3.3 29.5 + - - -
138A GLY* 4.2 9.0 - - - -
256A ASP* 3.8 13.7 - - - -
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Residues in contact with GLY 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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6A THR* 2.8 33.7 + - - +
7A LEU 4.1 3.6 - - - -
8A THR* 3.0 15.5 + - - -
40A GLY* 1.3 73.2 - - - +
42A ILE* 1.3 62.4 + - - +
44A VAL* 3.3 3.0 + - - -
45A ALA* 3.0 16.1 + - - +
135A VAL 4.7 0.2 - - - -
137A SER* 3.1 21.9 + - - -
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Residues in contact with ILE 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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8A THR* 2.8 14.9 + - - +
11A PRO* 3.7 23.1 - - + -
37A PRO* 3.8 28.9 - - + -
38A GLY 3.5 20.0 - - - +
39A GLY 3.7 6.7 - - - +
40A GLY 3.2 1.0 - - - -
41A GLY* 1.3 76.8 - - - +
43A ASN* 1.3 58.0 + - - +
45A ALA* 3.2 5.5 + - - +
46A ARG* 3.0 28.4 + - - +
57A ALA* 4.3 10.8 - - + -
59A PHE* 3.9 31.6 - - + -
69A LEU* 4.1 14.4 - - + -
73A LEU* 4.0 13.9 - - + -
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Residues in contact with ASN 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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37A PRO 3.8 7.4 + - - +
38A GLY* 4.4 4.2 - - - -
39A GLY 2.9 30.4 + - - +
42A ILE* 1.3 73.0 - - - +
44A VAL* 1.3 61.2 + - - +
46A ARG* 3.0 34.3 + - - -
47A ALA* 2.9 30.0 + - - +
253A GLY* 6.2 0.6 - - - -
256A ASP* 3.3 31.9 + - + +
294A LEU* 3.6 17.4 - - + +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.9 15.7 - - + -
40A GLY 2.9 21.2 + - - +
41A GLY* 3.6 8.5 - - - +
42A ILE 3.3 0.2 - - - -
43A ASN* 1.3 75.5 - - - +
45A ALA* 1.3 57.3 + - - +
47A ALA* 3.3 2.4 + - - +
48A ILE* 2.9 36.4 + - + +
135A VAL* 4.2 9.2 - - + -
137A SER* 4.2 10.8 - - - +
256A ASP* 3.8 24.0 - - + +
259A VAL* 3.8 28.3 - - + -
260A GLY* 3.8 19.5 - - - +
263A THR* 4.6 0.2 - - - +
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Residues in contact with ALA 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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6A THR* 4.0 10.3 - - - +
41A GLY 3.0 12.7 + - - +
42A ILE 3.2 8.9 + - - +
44A VAL* 1.3 77.7 - - - +
46A ARG* 1.3 61.0 + - - +
48A ILE* 3.4 3.9 + - - +
49A ALA* 3.1 21.7 + - - +
55A ALA* 3.9 29.1 + - + +
57A ALA* 4.2 7.4 - - + -
78A VAL* 3.9 24.0 - - + +
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Residues in contact with ARG 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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36A GLU* 5.2 7.7 - - - +
37A PRO* 3.9 35.8 + - - +
42A ILE* 3.0 17.6 + - - +
43A ASN* 3.0 32.9 + - - +
45A ALA* 1.3 74.1 - - - +
47A ALA* 1.3 64.8 + - - +
49A ALA* 3.2 4.4 + - - +
50A HIS* 3.0 38.2 + - + -
73A LEU* 4.0 12.3 - - + -
76A GLU* 2.6 43.4 + - - +
78A VAL* 4.2 11.2 - - + -
292A THR* 5.3 4.0 + - - -
294A LEU* 3.7 24.0 - - + +
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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 ASN 2.9 17.2 + - - +
44A VAL 3.6 4.5 - - - +
46A ARG* 1.3 76.5 - - - +
48A ILE* 1.3 64.3 + - - +
50A HIS* 3.1 8.7 + - - +
51A LEU* 3.0 29.4 + - + +
256A ASP 4.0 3.8 - - - +
257A SER* 3.8 34.3 - - - +
260A GLY* 4.6 2.2 - - - -
294A LEU* 3.7 9.1 - - + +
295A CYS* 4.1 9.6 - - - -
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Residues in contact with ILE 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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4A ILE* 4.0 19.3 - - + -
44A VAL* 2.9 34.4 + - + +
45A ALA 3.6 4.9 - - - +
46A ARG 3.2 0.2 - - - -
47A ALA* 1.3 76.8 - - - +
49A ALA* 1.3 61.4 + - - +
51A LEU* 3.1 8.9 + - - +
52A GLY 3.2 0.2 + - - -
53A GLY* 2.9 27.9 + - - -
54A SER* 3.5 35.9 - - - +
55A ALA* 3.8 17.9 - - + +
260A GLY* 3.5 27.8 - - - +
263A THR* 4.1 7.4 - - + -
264A LEU* 4.1 15.9 - - + -
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Residues in contact with ALA 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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45A ALA 3.1 12.9 + - - +
46A ARG 3.4 9.2 - - - +
48A ILE* 1.3 76.7 - - - +
50A HIS* 1.3 67.3 + - + +
52A GLY* 3.0 14.2 + - - -
53A GLY 3.5 13.3 - - - +
54A SER* 5.4 1.5 - - - +
76A GLU 5.0 6.7 - - - +
77A ASN 5.4 3.8 - - - +
78A VAL* 4.4 17.0 - - + -
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Residues in contact with HIS 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 ARG* 3.0 30.6 + - + -
47A ALA* 3.1 8.3 + - - +
49A ALA* 1.3 79.8 - - + +
51A LEU* 1.3 60.4 + - - +
52A GLY* 3.3 3.1 + - - -
76A GLU* 5.6 6.7 - - + -
294A LEU* 4.1 27.1 + - + +
295A CYS* 3.1 31.2 - - - +
296A SER* 4.8 4.7 - - - -
297A HIS* 3.4 21.1 + - - +
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Residues in contact with LEU 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 3.0 20.4 + - - +
48A ILE 3.1 4.6 + - - +
50A HIS* 1.3 76.7 - - - +
52A GLY* 1.3 58.2 + - - +
53A GLY 3.5 1.9 + - - -
257A SER 4.7 0.4 - - - +
260A GLY 4.6 0.9 - - - -
261A ALA* 3.7 39.5 - - + +
264A LEU* 3.9 15.8 - - + +
278A PHE* 4.0 16.7 - - + -
282A ALA* 4.2 2.0 - - + -
295A CYS* 3.8 19.7 - - - -
296A SER 4.2 0.7 - - - +
297A HIS* 3.9 31.8 - - + +
300A THR* 3.5 33.2 - - + +
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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