Contacts of the helix formed by residues 37 - 49 (chain A) in PDB entry 2ABQ
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A THR* 3.9 14.6 - - - -
8A ASN 4.9 3.4 - - - -
9A PRO* 4.5 3.8 - - - -
10A SER* 4.2 3.3 + - - -
12A ASP* 4.4 2.0 + - - -
36A GLY* 1.3 74.1 - - - -
38A LYS* 1.3 60.5 + - - -
39A GLY 3.4 2.5 - - - -
40A ILE 3.3 3.2 + - - -
41A ASN* 2.9 36.6 + - - +
88A ARG* 6.1 1.6 - - - -
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Residues in contact with LYS 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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6A THR* 4.6 2.0 - - - +
37A GLY* 1.3 70.5 - - - -
39A GLY* 1.3 63.9 + - - +
41A ASN* 3.3 0.9 + - - +
42A VAL* 3.0 29.9 + - - +
132A ALA* 3.7 21.0 + - + +
133A GLY* 3.4 28.6 - - - +
161A ASP* 3.3 28.9 + - - +
179A LYS* 5.6 0.2 - - - +
184A GLU* 6.0 1.6 - - - -
248A GLY* 4.6 4.6 - - - +
249A ASP* 2.7 44.4 + - - +
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Residues in contact with GLY 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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4A THR* 3.3 28.5 + - - +
5A VAL 3.9 10.8 - - - -
6A THR* 2.9 17.0 + - - -
38A LYS* 1.3 77.6 - - - +
40A ILE* 1.3 63.3 + - - +
42A VAL* 3.3 4.9 + - - +
43A SER 3.1 16.5 + - - -
130A VAL* 5.5 1.6 - - - -
132A ALA* 4.1 10.6 + - - -
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Residues in contact with ILE 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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4A THR* 4.8 0.9 - - - -
6A THR* 2.9 13.0 + - + +
9A PRO* 3.6 22.9 - - + -
35A PRO* 4.3 9.2 - - + +
36A GLY 3.2 23.6 - - - +
37A GLY 3.3 5.8 + - - +
39A GLY* 1.3 76.7 - - - +
41A ASN* 1.3 64.4 + - - +
43A SER* 2.9 23.6 + - - -
44A ARG* 2.9 31.9 + - - +
55A ALA* 5.1 2.2 - - + -
67A VAL* 3.9 21.8 - - + -
71A LEU* 4.2 16.2 - - + -
80A PHE* 4.1 22.2 - - + -
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Residues in contact with ASN 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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12A ASP* 4.5 4.0 + - - -
34A GLN* 4.3 5.1 + - - +
35A PRO 3.6 17.5 - - - +
36A GLY* 4.1 3.5 - - - -
37A GLY 2.9 37.9 + - - +
38A LYS 3.8 0.7 - - - +
40A ILE* 1.3 79.1 - - - +
42A VAL* 1.3 60.7 + - - +
44A ARG* 3.8 16.1 + - - +
45A VAL* 3.0 29.6 + - - +
245A VAL 4.3 10.9 + - - -
249A ASP* 3.7 27.9 + - + +
285A PHE* 4.4 18.2 - - + -
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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
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4A THR* 4.3 11.0 - - + -
38A LYS 3.0 16.5 + - - +
39A GLY* 3.7 7.6 - - - +
40A ILE 3.3 0.2 - - - -
41A ASN* 1.3 74.8 - - - +
43A SER* 1.3 57.9 + - - +
45A VAL* 3.8 0.4 - - - -
46A LEU* 2.8 44.2 + - + +
130A VAL* 4.5 14.1 - - + -
132A ALA* 5.1 3.6 - - + -
249A ASP* 3.6 33.0 - - + +
252A VAL* 4.1 26.9 - - + -
253A ALA* 3.8 15.8 - - + +
256A LEU* 4.9 0.9 - - + -
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Residues in contact with SER 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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4A THR* 3.0 26.3 + - - +
39A GLY 3.1 6.5 + - - -
40A ILE* 2.9 13.8 + - - -
42A VAL* 1.3 76.7 - - - +
44A ARG* 1.3 57.4 - - - +
46A LEU* 3.0 4.9 + - - +
47A LYS* 2.9 28.8 + - - +
53A THR* 2.8 31.8 + - - +
55A ALA* 3.9 9.1 - - - +
71A LEU* 5.7 1.6 - - - -
76A ILE* 4.1 17.3 - - - +
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Residues in contact with ARG 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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34A GLN* 3.6 35.0 - - - +
35A PRO* 3.8 24.4 + - - +
40A ILE* 2.9 36.2 + - + +
41A ASN* 3.8 11.0 + - - +
43A SER* 1.3 74.5 - - - +
45A VAL* 1.3 63.8 + - + +
47A LYS* 3.2 6.5 + - - +
48A ARG* 3.1 43.2 + - - +
71A LEU* 4.2 3.1 - - + -
74A GLU* 3.0 34.7 + - - +
76A ILE* 3.7 22.4 - - + -
285A PHE* 4.1 18.3 - - + -
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Residues in contact with VAL 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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41A ASN 3.0 20.9 + - - +
42A VAL* 4.7 0.4 - - - -
44A ARG* 1.3 74.1 - - + +
46A LEU* 1.3 66.1 + - - +
48A ARG* 3.0 10.8 + - + +
49A LEU* 3.0 27.2 + - + +
246A GLY 5.1 0.2 - - - +
249A ASP 5.3 0.2 - - - -
250A SER* 3.5 26.5 - - - +
253A ALA* 3.5 24.7 - - + -
285A PHE* 3.6 31.2 - - + -
286A CYS* 4.0 23.1 - - - -
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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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2A ILE* 3.8 26.7 - - + -
42A VAL* 2.8 31.2 + - + +
43A SER* 3.3 5.2 - - - +
45A VAL* 1.3 75.1 - - - +
47A LYS* 1.3 62.0 + - - +
49A LEU* 2.9 12.7 + - - +
50A GLY 3.1 0.7 + - - -
51A HIS* 2.8 42.9 + - + +
53A THR* 2.9 31.9 - - + -
253A ALA* 3.6 32.5 - - + +
256A LEU* 4.7 3.4 - - + -
257A ALA* 3.9 16.6 - - + +
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Residues in contact with LYS 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 SER 2.9 11.9 + - - +
44A ARG 3.2 10.8 - - - +
46A LEU* 1.3 76.7 - - - +
48A ARG* 1.3 60.0 + - + +
50A GLY* 2.8 20.4 + - - -
51A HIS 3.2 15.4 + - - +
52A GLU* 3.1 19.9 + - - +
74A GLU* 3.2 30.1 - - + +
75A GLU* 2.9 29.1 + - - +
76A ILE* 4.2 15.5 - - + -
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Residues in contact with ARG 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 ARG* 3.1 33.4 + - - +
45A VAL* 3.0 11.8 + - - +
47A LYS* 1.3 78.2 - - + +
49A LEU* 1.3 61.1 + - + +
50A GLY 3.2 1.0 + - - -
74A GLU* 3.1 26.8 + - - +
285A PHE* 4.2 26.6 - - - +
286A CYS 3.9 24.5 - - - +
287A THR* 5.0 1.5 - - - -
288A ARG* 4.0 18.4 + - - +
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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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45A VAL* 3.0 24.4 + - + +
46A LEU* 2.9 9.4 + - - +
48A ARG* 1.3 81.1 - - - +
50A GLY* 1.3 57.4 + - - +
51A HIS* 3.3 7.0 + - - -
253A ALA* 4.1 2.9 - - + -
254A GLY* 3.9 31.6 - - - +
257A ALA* 4.0 17.3 - - + -
271A PHE* 4.1 9.4 - - + -
275A ALA* 4.8 4.0 - - + -
286A CYS* 4.3 11.7 - - - +
287A THR 4.5 0.4 - - - -
288A ARG* 3.0 53.4 + - - +
291A VAL* 4.1 25.4 - - + -
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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