Contacts of the helix formed by residues 43 - 56 (chain a) in PDB entry 6QX2
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 43 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33a ARG 3.5 24.5 - - - +
34a ALA* 3.4 23.8 + - - +
35a LEU 4.1 2.9 - - - -
36a PRO* 4.1 18.6 - - + -
41a GLY 4.2 0.8 + - - -
42a LEU* 1.3 73.7 - - - +
44a PRO* 1.4 72.6 - - + +
45a VAL* 4.4 4.7 - - + +
46a HIS* 3.1 37.2 + - + +
47a ARG* 3.1 12.4 + - - +
172a ALA* 5.3 4.7 - - - -
173a SER 2.7 32.8 + - - +
174a GLY* 3.8 3.8 - - - -
5e G 3.6 4.2 + - - -
6e T 3.2 33.6 + - - +
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Residues in contact with PRO 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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31a VAL 4.9 3.1 - - - +
32a ALA* 3.6 35.9 - - + +
33a ARG* 4.1 10.1 - - - +
35a LEU 4.4 7.4 - - - +
42a LEU 4.5 0.9 - - - +
43a LYS* 1.4 87.3 - - + +
45a VAL* 1.3 63.6 + - - +
47a ARG* 3.2 17.8 + - - +
48a ARG* 2.9 54.3 + - - +
79a HIS* 4.6 3.8 - - + -
338a LEU* 6.0 1.8 - - + -
7e A 4.9 2.2 - - - +
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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
----------------------------------------------------------
33a ARG 5.3 0.2 - - - +
43a LYS* 4.4 4.7 - - + +
44a PRO* 1.3 78.5 - - - +
46a HIS* 1.3 73.2 - - + +
48a ARG* 3.6 2.2 + - - +
49a ILE* 3.1 43.4 + - + +
74a VAL* 5.2 0.4 - - + +
79a HIS* 3.4 40.1 - - + +
85a SER 4.3 0.2 - - - +
86a ILE* 4.1 17.7 - - + -
89a ALA* 4.0 18.6 - - + -
6e T 4.1 24.7 - - - +
7e A 3.9 6.7 + - - +
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Residues in contact with HIS 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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41a GLY 5.7 0.4 + - - -
42a LEU* 4.0 20.5 - - + +
43a LYS* 3.1 43.2 + - + +
45a VAL* 1.3 76.3 - - + +
47a ARG* 1.3 65.1 + - - +
49a ILE* 3.2 4.3 + - - +
50a LEU* 3.0 29.4 + - - +
89a ALA* 3.9 27.2 + - + +
92a ARG* 5.2 1.8 + - - -
93a MET* 3.9 28.6 - - + +
99a TYR* 3.9 17.7 + - - -
6e T 3.3 32.4 + - - -
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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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37a ASP* 3.6 13.5 - - - +
40a ASP* 2.9 31.9 + - - -
42a LEU* 3.0 37.5 + - + +
43a LYS 3.1 6.5 + - - +
44a PRO* 3.5 29.0 - - - +
46a HIS* 1.3 75.4 - - - +
48a ARG* 1.3 58.7 + - + +
50a LEU* 3.3 3.2 + - - +
51a TYR* 2.9 31.9 + - - +
157a PRO* 3.3 29.4 - - + +
158a SER 3.6 13.1 + - - -
159a VAL* 3.4 16.9 - - - +
160a LEU* 3.8 18.9 - - + +
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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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32a ALA* 5.7 4.6 + - - +
44a PRO* 2.9 31.4 + - - +
45a VAL 3.9 4.3 - - - +
47a ARG* 1.3 75.1 - - + +
49a ILE* 1.3 60.2 + - - +
51a TYR* 3.9 6.0 - - - +
52a GLY* 2.9 26.2 + - - -
74a VAL* 3.9 15.7 - - + +
78a TYR* 3.3 44.2 + - + -
79a HIS* 3.0 38.0 + - + +
80a PRO* 4.4 6.2 - - - +
81a HIS* 4.9 3.8 + - - -
147a ILE* 6.1 0.6 - - - +
150a TYR* 6.0 1.8 - - - +
156a GLU* 2.8 40.2 + - + +
157a PRO* 6.4 0.9 - - + -
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Residues in contact with ILE 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* 3.1 29.3 + - + +
46a HIS 3.2 6.3 + - - +
48a ARG* 1.3 74.8 - - - +
50a LEU* 1.3 59.2 + - - +
52a GLY* 3.2 2.9 + - - -
53a LEU* 2.9 40.9 + - + +
70a ILE* 4.9 4.4 - - + +
74a VAL* 3.9 14.8 - - + +
86a ILE* 3.5 40.2 - - + +
89a ALA* 4.1 2.5 - - + -
90a MET* 3.9 29.6 - - + +
93a MET* 3.6 28.0 - - + -
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Residues in contact with LEU 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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42a LEU* 4.1 16.4 - - + -
46a HIS 3.0 18.4 + - - +
47a ARG 3.9 3.4 - - - +
49a ILE* 1.3 75.1 - - - +
51a TYR* 1.3 61.3 + - - +
53a LEU* 3.4 19.4 + - + +
54a ASN* 3.2 22.2 + - - +
93a MET* 4.1 18.6 - - + -
103a LEU* 4.0 25.6 - - + +
104a VAL* 4.2 3.1 - - + -
128a MET* 5.2 0.2 - - - +
132a THR* 4.0 24.7 - - + -
135a LEU* 3.6 31.4 - - + -
136a LEU* 3.7 10.1 - - + +
160a LEU* 4.3 11.9 - - + -
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Residues in contact with TYR 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 18.4 + - - +
48a ARG* 3.9 4.3 - - - +
50a LEU* 1.3 73.6 - - - +
52a GLY* 1.3 59.8 - - - +
54a ASN* 3.2 9.3 + - - +
55a GLU* 2.9 68.6 + - + +
78a TYR* 3.6 27.1 - + - -
136a LEU* 4.4 4.4 - - + +
139a ILE* 3.7 17.9 - - + -
140a ASN* 6.1 0.9 - - - -
146a PHE* 3.6 23.7 - + - -
155a ARG* 3.6 19.2 + - - +
156a GLU* 4.8 0.7 - - + -
157a PRO* 3.4 42.0 - - + -
160a LEU* 5.0 2.7 - - + +
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Residues in contact with GLY 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 ARG 2.9 16.5 + - - -
49a ILE 3.2 4.2 + - - -
51a TYR* 1.3 73.1 - - - +
53a LEU* 1.3 63.9 + - - +
55a GLU* 3.5 3.2 + - - +
56a GLN* 3.2 30.0 + - - +
70a ILE* 5.8 1.8 - - - -
73a ASP* 3.8 9.8 - - - +
74a VAL* 4.4 5.8 - - - -
78a TYR* 4.0 17.5 - - - -
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Residues in contact with LEU 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 ILE* 2.9 28.1 + - + +
50a LEU* 3.5 28.3 - - + +
51a TYR 3.3 0.2 - - - -
52a GLY* 1.3 75.1 - - - +
54a ASN* 1.3 57.4 + - - +
57a GLY 3.3 3.1 + - - -
58a MET* 2.8 50.7 + - + +
70a ILE* 3.7 40.1 - - + +
90a MET* 5.4 1.6 - - + -
104a VAL* 4.4 9.9 - - + -
126a ALA* 5.1 0.4 - - + -
127a ARG* 4.3 12.1 - - - +
128a MET* 3.7 31.2 - - + +
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Residues in contact with ASN 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 LEU 3.2 10.7 + - - +
51a TYR* 3.2 10.5 + - - +
52a GLY 3.2 0.6 - - - -
53a LEU* 1.3 77.7 - - - +
55a GLU* 1.3 72.2 + - - +
57a GLY* 3.1 17.8 + - - -
59a THR* 5.0 3.8 - - - +
128a MET* 3.2 21.1 - - + +
133a LEU* 5.5 2.4 - - - +
136a LEU* 3.7 22.9 - - + +
139a ILE* 3.9 25.3 - - - +
140a ASN* 5.0 5.3 - - - +
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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 TYR* 2.9 63.1 + - + +
52a GLY 3.5 3.1 + - - +
54a ASN* 1.3 86.6 + - - +
56a GLN* 1.3 74.0 + - - +
57a GLY 3.3 2.1 + - - -
78a TYR* 3.6 13.5 - - - +
139a ILE* 5.7 0.2 - - - +
140a ASN* 5.2 7.6 + - - +
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Residues in contact with GLN 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 GLY 3.2 16.5 + - - +
54a ASN 3.3 0.2 - - - -
55a GLU* 1.3 91.6 + - - +
57a GLY* 1.3 64.2 + - - +
58a MET* 2.9 39.7 + - + +
69a ARG* 5.8 3.4 + - - +
73a ASP* 3.5 25.4 + - + +
77a LYS* 3.4 24.5 + - - +
78a TYR* 5.1 0.4 + - - -
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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