Contacts of the helix formed by residues 45 - 66 (chain K) in PDB entry 1P7G
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 45 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I ASN* 3.3 43.5 - - + +
41K LEU* 3.0 27.7 + - + +
44K GLN* 1.3 98.1 + - + +
46K HIS* 1.3 63.0 + - - +
48K GLN* 3.9 0.5 - - - +
49K GLY* 2.9 27.0 + - - -
221N LYS* 3.0 38.8 - - - +
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Residues in contact with HIS 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I GLU* 4.1 4.7 - - - -
183I TYR* 2.6 33.8 + + - -
188I ASN* 3.4 26.6 - - + +
41K LEU 3.1 20.7 + - - -
42K HIS* 3.3 20.9 - - + +
45K LYS* 1.3 75.8 - - - +
47K HIS* 1.3 67.3 + - - +
49K GLY* 2.9 12.0 + - - -
50K TYR* 3.2 29.0 + - + -
180K HIS* 3.3 47.1 + + + +
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Residues in contact with HIS 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.4 12.0 - - + +
21K PRO* 3.5 23.8 - - + +
42K HIS 2.9 17.4 + - - +
43K HIS* 3.5 13.9 + - - +
46K HIS* 1.3 71.8 - - - +
48K GLN* 1.3 62.2 + - - +
50K TYR* 3.0 19.9 + - - +
51K VAL* 3.1 8.1 + - + +
86K GLY 4.5 0.2 - - - -
87K HIS* 3.0 41.5 + - - -
90K HIS* 3.3 30.1 + + + +
91K SER* 3.6 10.3 - - - -
94K TRP* 2.8 27.3 + - - +
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Residues in contact with GLN 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 2.9 40.0 - - + +
43K HIS 3.2 4.7 + - - +
44K GLN 3.0 28.0 - - - +
45K LYS 4.0 0.9 - - - +
46K HIS 3.2 0.2 - - - -
47K HIS* 1.3 79.0 - - - +
49K GLY* 1.3 57.0 + - - +
51K VAL* 3.4 15.7 + - - +
52K ASN* 2.9 67.6 + - - +
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Residues in contact with GLY 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K LYS 2.9 18.1 + - - -
46K HIS* 2.9 6.4 + - - -
48K GLN* 1.3 77.9 - - - +
50K TYR* 1.3 59.8 + - - +
52K ASN* 3.7 8.9 - - - +
53K GLY* 3.0 22.7 + - - -
83K HIS* 3.9 4.9 + - - -
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Residues in contact with TYR 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K HIS* 3.2 29.8 + - + +
47K HIS* 3.0 12.8 + - - +
49K GLY* 1.3 74.2 - - - +
51K VAL* 1.3 62.5 + - - +
52K ASN 3.2 0.2 - - - -
54K ALA* 2.8 31.5 + - - +
82K PHE* 4.0 11.2 - + - -
83K HIS* 3.4 40.3 - + - +
86K GLY* 4.0 8.5 - - - -
87K HIS* 3.8 7.9 - - - +
90K HIS* 3.4 33.7 - + - -
161K HIS* 3.2 29.1 + + - -
178K TRP* 4.2 6.3 - + - -
180K HIS* 3.1 27.5 - - - -
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Residues in contact with VAL 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K TYR* 3.3 31.6 - - + +
19K THR* 3.7 15.9 - - - -
20K LEU* 3.9 10.5 - - + +
47K HIS* 3.1 16.0 + - + +
48K GLN* 3.6 18.2 - - - +
50K TYR* 1.3 77.4 - - - +
52K ASN* 1.3 59.0 + - - +
54K ALA* 3.2 7.0 + - - +
55K ASN* 3.0 32.0 + - - +
87K HIS* 3.3 38.8 - - + +
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Residues in contact with ASN 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K GLN* 2.9 50.8 + - - +
49K GLY* 3.7 8.4 - - - +
51K VAL* 1.3 78.3 - - - +
53K GLY* 1.3 56.9 + - - +
55K ASN* 3.4 6.7 + - - +
56K ALA* 2.8 30.1 + - - +
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Residues in contact with GLY 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K GLY 3.0 12.4 + - - -
52K ASN* 1.3 73.1 - - - +
54K ALA* 1.3 65.5 + - - +
56K ALA* 3.3 7.7 + - - +
57K ALA* 3.1 20.8 + - - +
79K ASP* 5.7 0.2 - - - +
83K HIS* 3.3 39.6 + - - -
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Residues in contact with ALA 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K TYR* 4.2 20.4 - - + -
50K TYR 2.8 20.3 + - - +
51K VAL* 3.4 7.4 - - - +
53K GLY* 1.3 72.1 - - - +
55K ASN* 1.3 63.4 + - - +
57K ALA* 3.0 7.4 + - - +
58K LEU* 3.0 25.6 + - - +
80K LEU* 3.8 11.4 - - + +
83K HIS* 3.2 15.3 - - + +
84K LEU* 4.1 15.3 - - + +
87K HIS* 5.4 1.6 - - + -
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Residues in contact with ASN 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K ARG* 3.4 31.1 + - - +
18K TYR* 2.7 55.7 + - - +
51K VAL* 3.0 25.1 + - - +
52K ASN* 3.9 5.6 + - - +
54K ALA* 1.3 77.0 - - - +
56K ALA* 1.3 62.3 + - - +
58K LEU* 3.2 6.7 + - - +
59K GLU* 3.0 23.2 + - - +
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Residues in contact with ALA 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K ASN 2.8 18.7 + - - +
53K GLY* 3.6 8.5 - - - +
55K ASN* 1.3 77.8 - - - +
57K ALA* 1.3 61.2 + - - +
59K GLU* 3.5 8.8 - - - +
60K LYS* 3.2 35.8 + - - +
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Residues in contact with ALA 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K GLY 3.1 11.4 + - - +
54K ALA 3.0 9.5 + - - +
56K ALA* 1.3 75.7 - - - +
58K LEU* 1.3 62.8 + - - +
59K GLU 3.2 0.2 - - - -
60K LYS* 3.3 5.5 + - - +
61K LEU* 3.1 28.1 + - - +
76K VAL* 3.4 24.0 - - + +
79K ASP* 4.5 6.5 - - + -
80K LEU* 4.0 31.2 - - + +
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Residues in contact with LEU 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J GLN* 4.1 7.2 - - - +
154J LEU* 3.8 28.5 - - + -
15K THR* 4.3 12.8 - - + +
16K LYS 3.6 14.6 - - - +
17K ARG* 3.8 17.2 + - - +
18K TYR* 3.5 35.0 - - + -
54K ALA 3.0 13.7 + - - +
55K ASN* 3.2 18.4 + - - +
57K ALA* 1.3 77.1 - - - +
59K GLU* 1.3 57.5 + - - +
61K LEU* 3.4 13.4 + - + +
62K GLU* 2.8 30.1 + - - +
65K ARG* 5.8 0.7 - - - +
80K LEU* 4.1 11.4 - - + -
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Residues in contact with GLU 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K ARG* 2.9 31.4 + - - +
55K ASN 3.0 12.5 + - - +
56K ALA* 3.5 14.4 - - - +
57K ALA 3.2 0.2 - - - -
58K LEU* 1.3 76.1 - - - +
60K LYS* 1.3 60.8 + - + +
62K GLU* 3.4 10.6 + - - +
63K LYS* 2.9 67.2 + - - +
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Residues in contact with LYS 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K ALA* 3.2 26.5 - - - +
57K ALA* 3.3 6.6 + - - +
59K GLU* 1.3 75.4 - - + +
61K LEU* 1.3 65.4 + - - +
63K LYS* 3.9 8.7 - - + +
64K PHE* 3.0 24.6 + - - +
69K ALA* 5.5 0.2 - - - +
70K GLN 5.0 1.7 - - - +
71K ILE* 4.0 6.7 - - + +
76K VAL* 4.0 32.2 - - + +
79K ASP* 4.3 15.8 + - - -
72L ASP* 5.5 5.1 + - - -
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Residues in contact with LEU 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J GLU* 3.5 27.4 - - - +
154J LEU* 5.3 0.9 - - + -
155J ILE 5.8 0.2 - - - +
15K THR* 5.5 0.2 - - + -
57K ALA 3.1 17.8 + - - +
58K LEU* 3.6 17.7 - - + +
60K LYS* 1.3 77.7 - - - +
62K GLU* 1.3 51.7 + - - +
64K PHE* 3.2 4.3 + - + +
65K ARG* 2.8 59.2 + - - +
71K ILE* 3.7 21.8 - - + -
73K ILE* 4.1 2.2 - - + -
76K VAL* 4.1 7.9 - - + -
77K LEU* 4.0 20.2 - - + -
80K LEU* 3.8 29.2 - - + -
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Residues in contact with GLU 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K VAL* 4.4 12.8 - - + -
14K THR* 4.6 0.9 - - - -
15K THR* 2.9 40.3 + - + +
17K ARG* 3.5 14.5 + - - -
58K LEU 2.8 17.6 + - - +
59K GLU* 3.6 14.2 - - - +
61K LEU* 1.3 73.6 - - - +
63K LYS* 1.3 65.1 + - + +
65K ARG* 3.2 7.0 + - - +
66K LYS* 2.9 63.9 + - + +
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Residues in contact with LYS 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K GLU* 2.9 50.6 + - - +
60K LYS* 3.9 7.9 - - + +
62K GLU* 1.3 78.6 - - + +
64K PHE* 1.3 59.6 + - - +
66K LYS 3.4 0.9 + - - -
67K GLY 3.4 1.9 + - - -
68K GLU* 2.9 52.2 + - + +
69K ALA* 3.3 20.4 + - + -
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Residues in contact with PHE 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J LYS* 3.3 22.6 + - + -
127J GLU* 3.2 39.7 - - + -
128J GLU* 3.7 44.9 - - + -
131J GLN* 6.0 3.6 - - + -
60K LYS 3.0 15.0 + - - +
61K LEU 3.3 8.1 - - - +
63K LYS* 1.3 76.9 - - - +
65K ARG* 1.3 56.1 + - - +
67K GLY* 2.8 26.2 + - - -
69K ALA* 3.6 23.3 - - - +
70K GLN* 4.5 9.4 - - - +
71K ILE* 3.5 45.3 - - + -
73K ILE* 5.2 0.4 - - + -
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Residues in contact with ARG 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J PHE* 3.1 34.5 + - - +
119J PHE* 3.5 23.4 - - + +
124J LYS* 3.4 39.3 - - + +
128J GLU* 2.7 41.4 + - - +
152J GLN* 5.4 1.2 + - - -
153J LEU 4.6 8.3 + - - -
154J LEU* 4.9 7.1 - - - +
155J ILE 4.9 3.2 - - - +
13K VAL* 3.6 27.1 - - + +
14K THR 4.2 0.8 + - - -
15K THR* 3.4 23.6 - - - +
61K LEU* 2.8 42.4 + - - +
62K GLU 3.7 0.4 - - - +
64K PHE* 1.3 69.4 - - + +
66K LYS* 1.3 57.5 + - - +
67K GLY 2.9 9.7 + - - -
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Residues in contact with LYS 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13K VAL* 3.7 34.3 - - + +
62K GLU* 2.9 53.1 + - + +
63K LYS* 5.0 0.2 - - - -
64K PHE 3.3 0.4 - - - -
65K ARG* 1.3 73.9 - - - +
67K GLY* 1.3 61.8 + - - +
68K GLU* 3.2 40.1 + - + +
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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
------------------------------------------------------------
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