Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 1K7E
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP* 1.4 72.9 - - - +
62A PRO* 1.3 78.9 - - - +
63A THR* 3.1 4.2 + - - -
64A ILE 3.4 2.6 + - - -
65A GLN* 2.9 22.0 + - - +
182A VAL* 3.6 9.2 - - - +
183A THR* 2.8 33.2 + - - -
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Residues in contact with PRO 62 (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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61A GLY* 1.3 85.5 - - - +
63A THR* 1.3 67.9 + - - +
65A GLN* 3.0 20.0 + - + +
66A ASN* 2.8 33.8 + - - +
182A VAL* 5.0 4.0 - - + -
183A THR 4.7 0.9 - - - +
184A GLY* 6.0 2.2 - - - -
172B GLU* 6.2 0.4 - - - +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 4.8 1.6 - - - -
62A PRO* 1.3 83.1 - - - +
64A ILE* 1.3 62.8 + - - +
66A ASN* 3.4 6.2 + - - +
67A ALA 3.1 17.2 + - - -
70A ARG* 4.6 0.3 + - - -
183A THR 6.3 0.4 - - - -
184A GLY* 5.9 2.2 - - - -
235A SER* 4.0 17.3 - - - +
238A VAL* 3.7 30.9 - - + +
239A LYS* 2.5 43.4 + - + +
242A GLU* 4.7 13.1 + - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.5 33.9 - - + -
24A THR* 4.8 2.7 - - - +
60A ASP* 2.8 38.8 - - + +
61A GLY 3.4 1.4 + - - -
62A PRO 3.3 0.4 - - - -
63A THR* 1.3 78.4 - - + +
65A GLN* 1.3 67.2 + - - +
67A ALA* 3.0 14.0 + - - +
68A ASN* 3.0 25.8 + - - +
183A THR* 3.6 10.5 - - - +
235A SER* 4.2 4.9 - - - +
238A VAL* 3.9 20.9 - - + -
401A IAG 3.3 31.0 - - + +
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 4.4 10.1 - - + -
60A ASP* 2.5 32.9 + - + +
61A GLY* 2.9 25.3 + - - +
62A PRO* 3.0 17.7 + - - +
64A ILE* 1.3 76.9 - - - +
66A ASN* 1.3 63.4 + - - +
68A ASN* 3.2 10.1 + - - +
69A LEU* 3.1 22.7 + - - +
161B SER* 3.9 24.8 - - - -
172B GLU* 4.4 6.3 + - - +
175B ARG* 2.8 40.9 + - - +
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 2.8 24.3 + - - +
63A THR* 3.5 10.3 - - - +
65A GLN* 1.3 70.7 - - - +
67A ALA* 1.3 61.5 + - - +
69A LEU* 3.0 7.2 + - - +
70A ARG* 2.7 51.6 + - + +
242A GLU* 4.6 16.4 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.3 23.6 - - - +
27A ASP* 3.5 19.7 - - - +
63A THR 3.1 6.2 + - - +
64A ILE* 3.0 12.3 + - - +
66A ASN* 1.3 78.9 - - - +
68A ASN* 1.4 56.9 + - - +
70A ARG* 3.2 13.3 + - - +
71A ALA* 2.8 29.6 + - - +
238A VAL* 3.5 22.7 - - + -
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Residues in contact with ASN 68 (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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24A THR* 4.0 10.6 + - - +
51A GLY 5.8 0.2 - - - -
52A VAL 4.3 2.1 - - - +
53A PRO* 3.1 25.4 - - - +
54A PHE 3.4 21.9 + - - +
57A PRO* 3.9 26.4 - - + +
60A ASP* 4.9 0.6 + - - -
64A ILE* 3.0 33.9 + - - +
65A GLN* 3.2 5.3 + - - +
67A ALA* 1.4 76.5 - - - +
69A LEU* 1.4 60.0 + - + +
71A ALA* 3.0 7.7 + - - +
72A PHE* 2.8 36.9 + - + -
102A TYR* 6.0 0.2 - - - -
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Residues in contact with LEU 69 (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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55A SER 5.9 1.8 - - - +
65A GLN 3.1 13.5 + - - +
66A ASN* 3.0 11.9 + - - +
68A ASN* 1.4 76.8 - - + +
70A ARG* 1.3 71.9 + - + +
72A PHE* 2.9 18.0 + - + +
73A ALA* 2.6 28.6 + - + +
161B SER* 6.1 0.9 - - - -
162B GLY* 4.3 30.1 - - - +
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Residues in contact with ARG 70 (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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26A GLY 4.9 0.2 - - - -
27A ASP* 2.6 45.6 + - - +
28A PRO* 3.9 17.1 - - + +
63A THR 4.6 0.2 + - - -
66A ASN* 2.7 36.0 + - + +
67A ALA* 3.4 10.9 - - - +
69A LEU* 1.3 81.4 - - + +
71A ALA* 1.3 64.3 + - - +
73A ALA* 3.2 13.6 + - - +
74A ALA 3.3 8.0 + - - -
238A VAL* 3.3 25.1 - - - +
241A ILE* 4.4 2.8 - - - +
242A GLU* 3.7 31.8 - - - +
245A LEU* 3.7 33.3 - - - +
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Residues in contact with ALA 71 (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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24A THR* 4.0 5.2 - - + -
25A LEU 3.8 12.8 - - - +
26A GLY 3.6 18.4 - - - +
27A ASP* 4.2 0.6 - - - +
53A PRO* 3.6 27.1 - - + -
67A ALA 2.8 17.0 + - - +
68A ASN 3.5 4.5 - - - +
70A ARG* 1.3 79.9 - - - +
72A PHE* 1.3 57.7 + - - +
74A ALA* 3.0 13.4 + - - -
76A VAL* 3.1 27.4 + - + +
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Residues in contact with PHE 72 (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 PRO* 3.6 9.9 - - + -
54A PHE 3.4 37.2 - - - -
55A SER* 3.9 8.5 - - - -
68A ASN* 2.8 25.7 + - + +
69A LEU* 3.6 19.3 - - + +
71A ALA* 1.3 72.2 - - - +
73A ALA* 1.3 68.4 + - - +
74A ALA 2.9 2.3 + - - -
75A GLY* 2.9 14.3 + - - +
76A VAL 3.9 20.4 - - - -
293B GLN* 3.5 41.7 - - + -
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Residues in contact with ALA 73 (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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69A LEU* 2.6 25.3 + - + +
70A ARG* 3.8 8.7 - - - +
72A PHE* 1.3 74.0 - - - +
74A ALA* 1.3 58.9 + - - +
75A GLY 3.6 0.3 + - - -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO 3.7 23.6 - - - +
29A GLY* 4.3 11.0 - - - -
30A ILE* 5.4 4.2 - - - +
70A ARG 3.3 2.9 + - - +
71A ALA 3.0 10.1 + - - +
72A PHE 2.9 1.0 - - - -
73A ALA* 1.3 82.5 - - - +
75A GLY* 1.3 61.9 + - - +
76A VAL* 3.2 8.1 + - + +
80A GLN* 5.0 0.9 - - - +
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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