Contacts of the helix formed by residues 42 - 56 (chain A) in PDB entry 6RKU
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 LYS 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ARG 4.3 9.0 - - - +
33A ALA* 3.4 29.8 - - - +
35A PRO* 4.6 10.0 - - + +
41A LEU* 1.3 76.4 - - - +
43A PRO* 1.3 75.3 - - + +
44A VAL* 3.1 6.4 + - + +
45A HIS* 3.2 24.4 + - + +
46A ARG* 3.1 18.6 + - - +
171A SER* 3.3 27.0 + - - +
172A SER 3.8 14.9 + - - -
173A GLY* 4.6 4.0 - - - -
11E G 3.1 13.7 + - - -
12E T 2.8 40.7 + - - +
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Residues in contact with PRO 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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30A VAL 5.5 1.3 - - - +
31A GLY* 3.2 31.0 - - - +
32A ARG 4.1 10.1 - - - +
34A LEU 5.1 6.5 - - - +
41A LEU 3.9 2.2 - - - +
42A LYS* 1.3 87.6 - - + +
44A VAL* 1.3 58.0 + - + +
46A ARG* 3.2 15.6 + - + +
47A ARG* 2.9 49.6 + - - +
78A HIS* 5.6 0.9 - - + -
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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
----------------------------------------------------------
32A ARG 5.8 2.0 - - - +
42A LYS* 3.1 4.8 + - + +
43A PRO* 1.3 79.4 - - + +
45A HIS* 1.3 68.2 + - + +
47A ARG* 3.3 3.5 + - - +
48A VAL* 2.9 37.7 + - + +
73A VAL* 6.5 0.2 - - + -
78A HIS* 3.4 37.2 - - + +
84A ALA 5.9 0.2 - - - -
85A VAL* 5.0 9.9 - - + -
88A THR* 4.1 28.9 - - + +
12E T 3.8 11.9 - - - +
13E A 3.6 22.7 - - - +
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Residues in contact with HIS 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 LEU* 4.5 19.3 - - + -
42A LYS* 3.2 33.0 + - + +
44A VAL* 1.3 78.2 - - + +
46A ARG* 1.3 63.2 + - - +
48A VAL* 3.4 5.6 + - - +
49A LEU* 2.9 35.0 + - + +
88A THR* 3.4 25.1 - - + +
91A ARG* 5.2 7.6 + - - -
92A MET* 3.4 38.1 - - + +
102A LEU* 6.2 1.1 - - + -
12E T 3.5 26.1 + - - -
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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
----------------------------------------------------------
36A ASP* 4.0 13.5 + - - -
39A ASP* 2.4 33.6 + - - -
41A LEU* 4.1 17.0 + - + +
42A LYS 3.1 10.5 + - - +
43A PRO* 3.3 18.3 - - - +
45A HIS* 1.3 77.3 - - - +
47A ARG* 1.3 61.0 + - + +
49A LEU* 3.3 3.3 + - - +
50A TYR* 2.9 29.0 + - + +
155A ILE* 4.9 7.4 - - + -
156A PRO* 3.5 15.7 + - + +
157A ASP 3.0 25.5 + - - -
158A VAL* 3.2 4.4 - - - +
159A MET* 3.0 56.8 - - + +
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Residues in contact with ARG 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 PRO* 2.9 32.6 + - + +
44A VAL* 3.9 3.4 - - - +
46A ARG* 1.3 77.8 - - + +
48A VAL* 1.3 57.4 + - - +
50A TYR* 3.4 7.2 + - - +
51A ALA* 2.9 31.1 + - - +
73A VAL* 4.8 4.2 - - + +
77A TYR* 3.0 49.8 + - + +
78A HIS* 3.7 32.8 - - + +
79A PRO* 4.5 4.4 - - - +
80A HIS* 5.1 5.7 - - - -
155A ILE* 4.7 25.7 - - + +
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Residues in contact with VAL 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 VAL* 2.9 33.4 + - + +
45A HIS* 3.8 6.3 - - - +
46A ARG 3.3 0.2 - - - -
47A ARG* 1.3 77.7 - - - +
49A LEU* 1.3 64.7 + - + +
51A ALA* 3.3 2.8 + - - +
52A MET* 2.9 50.5 + - + +
69A VAL* 5.0 4.0 - - + -
73A VAL* 4.4 24.4 - - + +
85A VAL* 4.5 12.8 - - + +
88A THR* 5.7 1.8 - - + -
89A ILE* 4.4 17.5 - - + -
92A MET* 4.7 11.2 - - + -
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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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41A LEU* 4.8 20.0 - - + -
45A HIS* 2.9 26.8 + - + +
46A ARG* 3.8 3.6 - - - +
48A VAL* 1.3 79.3 - - + +
50A TYR* 1.3 63.6 + - - +
52A MET* 3.3 8.7 + - - +
53A ASN* 2.9 24.3 + - - +
92A MET* 5.6 5.6 - - + -
102A LEU* 4.9 23.8 - - + -
103A VAL* 5.2 9.0 - - + -
127A LEU* 4.2 24.6 - - + +
131A ALA* 5.4 5.6 - - + -
134A LEU* 5.5 10.5 - - + -
135A MET* 3.7 24.1 - - + +
159A MET* 4.8 4.7 - - + -
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Residues in contact with TYR 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* 2.9 17.9 + - + +
47A ARG* 3.8 7.4 - - - +
49A LEU* 1.3 75.8 - - - +
51A ALA* 1.3 58.9 + - - +
53A ASN* 3.3 2.0 + - + +
54A VAL* 2.9 56.1 + - + +
77A TYR* 3.5 37.6 + + - -
135A MET* 3.8 10.0 - - + +
138A LEU* 4.0 23.1 - - + -
145A PHE* 5.5 6.7 - + - -
154A LYS* 4.0 17.2 + - - +
155A ILE* 5.2 3.4 - - + -
156A PRO* 3.6 38.5 - - + +
159A MET* 4.2 6.7 - - + -
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Residues in contact with ALA 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 ARG 2.9 17.8 + - - +
48A VAL 3.7 4.0 - - - +
50A TYR* 1.3 80.3 - - - +
52A MET* 1.3 57.8 + - + +
54A VAL* 3.3 5.8 + - - +
55A LEU* 2.9 32.0 + - - +
69A VAL* 5.6 2.2 - - + -
72A ASP* 4.0 18.0 - - + +
73A VAL* 3.8 24.0 - - + -
76A LYS* 6.2 0.2 - - - +
77A TYR* 4.6 13.2 - - + -
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Residues in contact with MET 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 VAL* 2.9 40.7 + - + +
49A LEU* 3.3 8.0 + - - +
51A ALA* 1.3 76.3 - - - +
53A ASN* 1.3 60.9 + - - +
55A LEU* 3.6 5.9 + - - +
56A GLY 3.4 14.4 + - - -
57A ASN* 3.4 23.6 + - + +
69A VAL* 4.0 23.6 - - + -
89A ILE* 4.9 5.6 - - + -
103A VAL* 4.5 20.4 - - + -
125A ILE* 3.6 31.0 - - + -
126A ARG* 5.6 2.7 - - - -
127A LEU* 3.6 38.8 - - + -
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Residues in contact with ASN 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 LEU 2.9 17.3 + - - +
50A TYR* 3.7 2.2 - - + +
52A MET* 1.3 75.9 - - - +
54A VAL* 1.3 67.1 + - + +
56A GLY* 3.2 14.2 + - - -
57A ASN 5.2 0.7 - - - +
58A ASP* 4.9 8.6 - - - +
127A LEU* 4.8 9.8 - - + +
132A HIS* 5.7 5.7 - - - -
135A MET* 3.4 42.5 + - + +
138A LEU* 4.1 13.3 - - + +
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Residues in contact with VAL 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 TYR* 2.9 58.5 + - + +
51A ALA* 3.9 5.4 - - - +
53A ASN* 1.3 78.5 - - + +
55A LEU* 1.3 63.1 + - - +
56A GLY* 3.3 1.2 + - - -
76A LYS* 4.5 19.1 - - - +
77A TYR* 4.8 4.3 - - - +
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Residues in contact with LEU 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 ALA 2.9 17.5 + - - +
52A MET* 3.9 6.5 - - - +
54A VAL* 1.3 78.3 - - - +
56A GLY* 1.3 60.9 + - - +
57A ASN* 4.2 8.1 - - + +
64A LYS* 3.7 37.5 - - + +
68A ARG* 4.8 28.5 - - + +
69A VAL* 4.8 19.1 - - + -
72A ASP* 5.2 18.8 - - + +
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Residues in contact with GLY 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 MET 3.4 0.6 + - - -
53A ASN 3.2 12.7 + - - -
54A VAL 3.1 4.7 - - - -
55A LEU* 1.3 81.0 - - - +
57A ASN* 1.3 59.8 + - - +
58A ASP* 3.7 6.2 + - - -
61A LYS* 3.2 30.2 + - - +
64A LYS* 4.8 5.2 - - - -
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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