Contacts of the helix formed by residues 41 - 57 (chain A) in PDB entry 4QKB
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 SER 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 1.3 76.4 - - - +
42A THR* 1.3 55.9 + - - +
43A ALA* 3.9 8.9 + - - +
44A GLU* 3.0 35.8 + - - +
45A GLU* 2.8 34.2 + - - +
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Residues in contact with THR 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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41A SER* 1.3 70.7 - - - +
43A ALA* 1.3 65.1 + - - +
45A GLU* 3.1 17.5 + - - +
46A GLU* 2.9 47.2 + - - +
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Residues in contact with ALA 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 SER* 3.2 8.1 + - - +
42A THR* 1.3 78.5 - - - +
44A GLU* 1.3 54.7 + - + +
46A GLU* 3.3 8.9 + - - +
47A THR* 2.7 41.3 + - - +
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Residues in contact with GLU 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 PHE 3.8 0.5 - - - +
40A LEU* 3.6 13.1 - - + -
41A SER* 3.0 39.0 + - - +
43A ALA* 1.3 75.5 - - + +
45A GLU* 1.3 65.6 + - - +
47A THR* 3.5 7.9 + - - -
48A LEU* 3.1 29.6 + - - +
87A ALA* 6.1 0.2 - - - +
88A ILE* 3.6 24.0 + - + +
91A ARG* 2.7 44.8 + - - -
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Residues in contact with GLU 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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40A LEU* 4.2 10.5 - - + +
41A SER 2.8 20.0 + - - +
42A THR* 3.3 16.5 + - + +
44A GLU* 1.3 72.3 - - - +
46A GLU* 1.3 58.3 + - + +
48A LEU* 3.2 6.0 + - - +
49A SER* 2.9 28.2 + - - -
137A LEU* 3.9 22.9 - - + +
138A LEU* 4.7 2.9 + - - -
161A PRO* 3.6 24.8 - - - +
162A GLY* 3.9 29.9 + - - -
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Residues in contact with GLU 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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42A THR* 2.9 37.2 + - + +
43A ALA* 3.7 7.3 - - - +
45A GLU* 1.3 76.1 - - + +
47A THR* 1.3 66.3 + - - +
49A SER* 3.1 6.7 + - - -
50A ARG* 2.8 59.7 + - + +
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Residues in contact with THR 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 ALA* 2.7 27.5 + - - +
44A GLU* 3.5 9.9 - - - -
46A GLU* 1.3 72.2 - - - +
48A LEU* 1.3 62.5 + - - +
50A ARG* 3.7 6.0 + - - +
51A GLU* 3.3 23.0 + - - +
82A SER* 5.2 0.9 - - - +
84A ALA* 3.7 30.5 - - + +
85A SER* 4.0 17.7 - - - +
88A ILE* 4.1 8.7 - - + -
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Residues in contact with LEU 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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40A LEU* 3.8 28.5 - - + -
44A GLU 3.1 14.5 + - - +
45A GLU 3.5 7.0 - - - +
46A GLU 3.1 0.2 - - - -
47A THR* 1.3 74.5 - - - +
49A SER* 1.3 64.3 + - - +
51A GLU* 3.3 3.2 + - + -
52A LEU* 3.1 41.5 + - + +
81A TRP* 4.3 18.4 - - + -
85A SER* 3.8 20.2 - - - +
88A ILE* 4.0 19.7 - - + -
89A MSE 5.1 5.2 - - - -
135A LEU* 3.9 17.3 - - + -
137A LEU* 3.8 19.7 - - + -
200A VAL* 4.8 7.2 - - + -
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Residues in contact with SER 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 GLU 2.9 14.3 + - - -
46A GLU* 3.6 12.1 - - - -
48A LEU* 1.3 74.2 - - - +
50A ARG* 1.3 72.8 + - - +
52A LEU* 5.2 2.0 - - - -
53A GLU* 3.0 35.4 + - - +
137A LEU* 4.6 9.8 - - - +
138A LEU* 3.6 27.0 - - - +
198A ILE* 5.2 7.3 - - - +
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Residues in contact with ARG 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 GLU* 2.8 60.1 + - + +
47A THR* 3.9 6.3 - - - +
49A SER* 1.3 79.7 - - - +
51A GLU* 1.3 62.7 + - - +
53A GLU* 4.5 1.1 - - - +
54A PRO* 3.1 22.2 - - - +
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Residues in contact with GLU 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 THR* 3.3 12.3 + - - +
48A LEU 3.3 5.1 + - - +
50A ARG* 1.3 80.1 - - - +
52A LEU* 1.3 64.4 + - + +
54A PRO* 3.8 10.4 - - - +
55A GLU* 3.9 11.6 - - - +
78A LYS* 3.3 31.4 + - - +
80A ARG 4.1 0.2 - - - +
81A TRP* 3.7 1.5 - - - -
82A SER* 2.6 48.1 + - - -
85A SER* 2.6 25.0 + - - +
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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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48A LEU* 3.1 30.0 + - + +
49A SER* 4.5 1.1 - - - +
51A GLU* 1.3 77.8 - - + +
53A GLU* 1.3 66.5 + - - +
54A PRO 3.4 0.9 - - - -
55A GLU* 3.0 9.9 + - - +
56A LEU* 2.9 36.7 + - + +
76A THR* 5.6 1.3 - - + -
78A LYS* 3.6 33.2 - - + -
81A TRP* 4.0 10.8 - - + -
109A VAL* 3.8 25.6 - - + -
137A LEU* 4.5 1.6 - - + -
198A ILE* 4.2 13.5 - - + -
200A VAL* 3.9 26.5 - - + -
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Residues in contact with GLU 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 SER* 3.0 23.5 + - - +
50A ARG* 4.5 0.9 - - - +
52A LEU* 1.3 77.7 - - - +
54A PRO* 1.4 62.9 - - + +
56A LEU* 3.4 6.4 + - - +
57A ARG* 2.8 54.7 + - + +
138A LEU* 5.0 2.3 - - - +
196A ARG* 2.9 39.2 + - - -
198A ILE* 4.0 8.6 - - + +
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Residues in contact with PRO 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 ARG 3.1 22.2 - - - +
51A GLU* 3.8 7.4 - - - +
52A LEU 3.5 1.6 - - - -
53A GLU* 1.4 94.7 - - + +
55A GLU* 1.3 61.2 + - - +
57A ARG* 4.1 6.9 - - + +
58A ARG* 3.6 26.7 + - - +
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Residues in contact with GLU 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 GLU* 3.9 10.6 - - - +
52A LEU* 3.0 13.8 + - - +
54A PRO* 1.3 82.8 - - - +
56A LEU* 1.3 61.6 + - + +
58A ARG* 3.7 13.8 + - - +
59A ARG* 4.5 12.9 + - - +
76A THR* 3.9 28.2 + - + +
77A GLU 5.1 0.5 - - - +
78A LYS* 2.9 48.7 + - - +
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Residues in contact with LEU 56 (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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52A LEU* 2.9 21.5 + - + +
53A GLU 3.9 2.5 - - - +
55A GLU* 1.3 73.2 - - - +
57A ARG* 1.3 52.0 + - - +
58A ARG 3.0 4.9 - - - -
59A ARG* 2.8 39.3 + - - +
74A ARG* 3.6 11.4 - - + +
75A GLU* 4.3 19.1 - - - +
76A THR* 4.1 23.6 - - + -
109A VAL* 4.0 22.0 - - + +
111A ASP* 3.9 34.8 - - + +
196A ARG* 4.4 3.4 - - - +
198A ILE* 3.8 31.0 - - + -
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Residues in contact with ARG 57 (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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53A GLU* 2.8 48.9 + - + +
54A PRO* 4.1 7.9 - - + +
55A GLU 3.5 0.2 - - - -
56A LEU* 1.3 71.2 - - - +
58A ARG* 1.3 59.4 + - - +
59A ARG 3.2 6.2 + - - +
74A ARG* 4.0 18.1 + - - +
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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