Contacts of the helix formed by residues 63 - 73 (chain A) in PDB entry 1SEK
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A VAL* 1.3 76.9 - - - +
64A GLU* 1.3 64.7 + - - -
66A HIS* 3.1 19.4 + - - +
67A ASP* 3.3 15.8 + - - +
311A ARG* 4.6 13.2 - - - +
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Residues in contact with GLU 64 (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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62A VAL 3.7 0.4 + - - -
63A GLY* 1.3 70.3 - - - -
65A SER* 1.3 64.2 + - - +
67A ASP* 3.0 12.3 + - - +
68A GLU* 2.9 23.6 + - - +
303A LYS* 3.5 31.6 - - + -
309A ALA 5.8 0.2 - - - +
311A ARG* 5.9 0.8 - - - +
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Residues in contact with SER 65 (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 SER* 3.6 10.9 + - - -
62A VAL 4.0 3.9 + - - -
63A GLY 3.4 0.6 - - - -
64A GLU* 1.3 77.4 - - - +
66A HIS* 1.3 58.5 + - - +
68A GLU* 3.4 4.6 + - - +
69A LEU* 3.1 35.7 + - - +
303A LYS* 3.5 21.7 - - - +
304A LEU* 4.3 8.0 + - - +
309A ALA 3.5 15.3 + - - -
310A ALA* 2.9 31.4 + - - -
311A ARG* 6.0 0.2 - - - +
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Residues in contact with HIS 66 (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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58A ALA* 2.8 29.6 - - + -
61A SER* 3.7 15.8 - - - -
62A VAL* 3.7 21.9 + - - +
63A GLY 3.1 12.5 + - - +
65A SER* 1.3 77.5 + - - +
67A ASP* 1.3 78.3 + - - +
69A LEU* 3.4 5.4 + - - +
70A LEU* 3.0 50.9 + - + +
78A ASP* 2.7 32.4 + - - -
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Residues in contact with ASP 67 (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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63A GLY* 3.7 15.0 - - - +
64A GLU* 3.0 9.4 + - - +
66A HIS* 1.3 90.8 + - - +
68A GLU* 1.3 56.9 + - - +
70A LEU* 3.7 6.7 - - - +
71A ARG* 2.7 53.9 + - - +
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Residues in contact with GLU 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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64A GLU 2.9 10.0 + - - +
65A SER* 3.4 8.9 - - - +
67A ASP* 1.3 77.6 - - - +
69A LEU* 1.3 62.9 + - + +
71A ARG* 3.2 8.5 + - - +
72A ALA* 2.9 25.7 + - - +
300A ASN* 3.4 31.0 + - - +
301A ILE* 4.0 7.5 - - + +
302A LYS* 3.4 13.0 + - - +
303A LYS* 3.3 53.5 + - + +
304A LEU 4.5 1.2 + - - -
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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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54A LEU* 3.5 47.6 - - + +
57A LEU* 4.0 2.0 - - + +
58A ALA* 4.0 22.0 - - + +
61A SER* 3.7 22.9 - - - +
65A SER* 3.1 16.9 + - - +
66A HIS 3.7 4.3 - - - +
68A GLU* 1.3 79.9 - - + +
70A LEU* 1.3 57.3 + - - +
72A ALA* 3.3 5.1 + - - +
73A LEU* 2.9 35.2 + - + +
301A ILE* 4.2 21.3 - - + +
304A LEU* 3.9 22.2 - - + -
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Residues in contact with LEU 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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58A ALA* 4.0 21.3 - - + -
66A HIS* 3.0 42.1 + - + +
67A ASP* 3.7 6.3 - - - +
69A LEU* 1.3 75.8 - - - +
71A ARG* 1.3 65.1 + - - +
73A LEU* 3.0 4.8 + - + -
74A ALA 2.9 18.5 + - - -
75A LEU* 3.1 35.0 + - + +
76A PRO 3.7 18.8 - - - +
77A ASN* 3.7 12.1 - - - +
78A ASP* 4.6 3.6 - - - +
81A THR* 3.6 24.5 - - + +
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Residues in contact with ARG 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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25A GLN* 5.9 0.2 - - - -
67A ASP* 2.7 39.6 + - - +
68A GLU* 3.4 7.6 - - - +
70A LEU* 1.3 72.2 - - - +
72A ALA* 1.3 57.3 + - - +
74A ALA* 3.0 20.6 + - - +
75A LEU 5.2 1.3 - - - -
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Residues in contact with ALA 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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25A GLN* 3.2 22.9 + - - +
26A PHE* 3.4 16.9 - - + -
29A GLN* 5.2 4.6 + - - +
68A GLU 2.9 16.5 + - - +
69A LEU 3.7 2.5 - - - +
71A ARG* 1.3 75.8 - - - +
73A LEU* 1.3 58.8 + - + +
74A ALA 3.1 0.7 - - - -
299A MET* 4.5 10.3 - - + +
300A ASN* 5.8 1.3 - - + +
301A ILE* 3.6 33.4 - - + -
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Residues in contact with LEU 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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22A SER* 3.1 20.5 + - - -
25A GLN* 4.0 2.5 - - - +
26A PHE* 4.2 6.5 - - + -
51A LEU* 3.9 30.5 - - + +
54A LEU* 3.9 29.2 - - + +
55A GLY* 4.0 30.7 - - - +
58A ALA* 4.9 5.4 - - + -
69A LEU* 2.9 25.9 + - + +
70A LEU* 3.0 7.8 + - + +
72A ALA* 1.3 76.6 - - + +
74A ALA* 1.3 70.9 + - - +
75A LEU* 3.3 28.1 + - + +
85A PHE* 5.0 3.4 - - + -
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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