Contacts of the helix formed by residues 57 - 70 (chain A) in PDB entry 4KAL
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN 3.4 23.6 - - - -
11A ILE* 3.7 6.0 + - - +
56A GLY* 1.3 70.4 - - - +
58A SER* 1.3 67.9 + - - -
59A ALA 3.4 2.2 - - - -
60A GLY* 3.0 5.1 + - - -
61A ASN* 2.8 27.1 + - - -
88A PHE* 5.1 0.7 - - - -
154A GLU* 4.0 0.2 - - - -
401A ADN 2.8 22.4 + - - -
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Residues in contact with SER 58 (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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57A GLY* 1.3 70.8 - - - +
59A ALA* 1.3 57.9 + - - +
61A ASN* 3.3 4.9 + - - +
62A THR* 3.0 28.3 + - - -
152A TYR* 4.8 2.1 + - - -
154A GLU* 3.2 18.9 + - - +
156A TYR* 4.1 14.2 - - - -
184A THR* 4.6 11.6 - - - +
186A SER* 5.9 0.9 - - - -
276A ASP* 2.5 35.3 + - - -
401A ADN 3.3 22.6 + - - -
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Residues in contact with ALA 59 (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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6A THR* 2.8 30.7 + - - +
7A VAL 3.4 33.9 - - - +
8A GLY* 3.8 2.7 - - - +
58A SER* 1.3 70.6 + - - +
60A GLY* 1.3 59.8 + - - +
62A THR* 3.2 7.5 + - - -
63A ALA 2.9 19.2 + - - -
75A TYR* 3.8 1.3 - - + -
152A TYR* 4.5 7.9 - - + -
154A GLU* 2.7 23.4 + - + +
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Residues in contact with GLY 60 (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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56A GLY 4.2 2.0 - - - -
57A GLY 3.0 9.4 + - - -
59A ALA* 1.3 77.7 - - - +
61A ASN* 1.3 56.0 + - - +
63A ALA* 3.3 4.3 + - - +
64A ALA* 2.9 29.3 + - - +
75A TYR* 3.4 25.4 + - - -
92A ILE* 4.0 9.4 - - - +
313A ARG* 3.7 18.1 + - - -
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Residues in contact with ASN 61 (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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56A GLY* 3.5 10.2 - - - -
57A GLY 2.8 19.2 + - - +
58A SER 3.4 5.8 - - - +
60A GLY* 1.3 70.9 - - - -
62A THR* 1.3 57.8 + - - +
64A ALA* 3.3 2.9 + - - +
65A GLY* 2.9 26.5 + - - -
276A ASP* 3.0 29.4 + - + +
277A LEU* 4.1 8.0 - - + +
280A SER* 3.8 1.0 + - - -
312A PRO* 3.3 26.4 + - - +
313A ARG* 2.8 31.7 + - - +
401A ADN 3.0 25.1 + - - -
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Residues in contact with THR 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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6A THR* 4.0 11.0 - - + -
58A SER 3.0 10.4 + - - -
59A ALA 3.2 8.0 + - - -
61A ASN* 1.3 76.5 - - - +
63A ALA* 1.3 63.3 + - - +
65A GLY 3.2 0.3 + - - -
66A VAL* 3.0 15.2 + - + +
152A TYR* 3.9 30.2 + - + -
276A ASP* 2.7 27.0 + - - +
279A ALA* 4.1 5.6 - - + -
280A SER* 2.7 41.7 + - - +
283A LEU* 4.5 6.5 - - + -
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Residues in contact with ALA 63 (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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4A VAL* 5.9 0.2 - - - -
6A THR* 3.4 26.8 - - + +
59A ALA 2.9 11.4 + - - +
60A GLY 3.6 5.4 - - - +
62A THR* 1.3 73.0 - - - +
64A ALA* 1.3 64.4 + - - +
66A VAL* 3.2 3.9 + - - -
67A ALA* 3.0 20.3 + - - +
73A ALA* 3.5 15.0 - - + +
74A ALA 4.1 8.5 - - - +
75A TYR* 4.4 4.7 - - + -
92A ILE* 4.6 0.7 - - + -
97A VAL* 3.9 24.9 - - + -
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Residues in contact with ALA 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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60A GLY 2.9 17.2 + - - +
61A ASN 3.6 4.9 - - - +
63A ALA* 1.3 75.1 - - - +
65A GLY* 1.3 58.2 + - - +
67A ALA 3.3 1.2 + - - -
68A ASN* 2.9 28.8 + - - +
92A ILE* 5.3 1.3 - - + -
95A GLN* 3.4 30.4 - - + +
97A VAL* 4.0 6.7 - - + +
313A ARG* 3.7 33.2 - - + +
314A PRO* 6.5 0.4 - - + -
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Residues in contact with GLY 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 ASN 2.9 10.7 + - - -
62A THR 3.2 0.2 + - - -
63A ALA 3.2 0.2 - - - -
64A ALA* 1.3 74.5 - - - +
66A VAL* 1.3 62.5 + - - +
68A ASN* 3.3 8.6 + - - +
69A LEU* 3.0 28.1 + - - +
277A LEU* 3.7 18.8 - - - -
280A SER* 3.4 20.6 - - - -
314A PRO* 5.5 2.8 - - - +
318A LEU* 3.7 1.8 - - - +
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Residues in contact with VAL 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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3A ASP* 5.0 2.2 - - + -
4A VAL* 4.1 37.0 - - + -
62A THR* 3.0 22.4 + - + +
63A ALA* 3.6 7.0 - - - +
65A GLY* 1.3 75.5 - - - +
67A ALA* 1.3 60.5 + - - +
69A LEU* 3.2 8.4 + - - +
70A GLY 3.2 5.4 + - - -
71A GLY* 3.0 43.9 + - - -
72A LYS 4.3 1.6 - - - +
73A ALA* 4.1 11.7 - - + -
280A SER* 3.8 24.0 - - - +
283A LEU* 4.8 1.3 - - + -
284A TYR* 4.7 9.9 - - + +
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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
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63A ALA 3.0 12.5 + - - +
64A ALA 3.6 7.9 - - - +
66A VAL* 1.3 76.1 - - - +
68A ASN* 1.3 63.5 + - - +
70A GLY* 3.1 13.5 + - - -
71A GLY 3.5 14.8 - - - +
73A ALA* 4.3 4.4 - - + +
95A GLN* 3.4 27.1 - - + +
96A GLY 4.5 7.2 - - - +
97A VAL* 3.8 15.3 - - + -
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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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64A ALA 2.9 17.3 + - - +
65A GLY* 3.4 8.1 - - - +
67A ALA* 1.3 76.9 - - - +
69A LEU* 1.3 60.7 + - - +
70A GLY* 3.3 1.4 + - - -
95A GLN* 3.7 21.3 + - - +
314A PRO* 3.6 19.4 + - - +
316A THR 3.1 19.6 + - - -
317A SER* 3.6 6.1 + - - -
318A LEU* 2.7 41.9 + - + +
319A SER* 3.9 12.5 + - - -
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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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65A GLY 3.0 18.6 + - - +
66A VAL* 3.2 7.2 + - - +
68A ASN* 1.3 75.5 - - - +
70A GLY* 1.3 57.5 + - - +
71A GLY 3.6 0.2 - - - -
280A SER* 3.9 4.9 - - - +
281A GLY* 3.7 30.1 - - - +
284A TYR* 3.6 49.1 + - + -
298A LEU* 4.8 7.2 - - + +
301A LEU* 5.9 2.7 - - + -
302A ALA* 4.9 4.9 - - + -
318A LEU* 3.7 39.0 - - + +
319A SER* 3.6 20.6 - - - +
322A ALA* 4.4 14.4 - - + -
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Residues in contact with GLY 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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67A ALA 3.1 12.7 + - - -
68A ASN 3.2 1.3 - - - -
69A LEU* 1.3 79.2 - - - +
71A GLY* 1.3 64.0 + - - +
72A LYS* 4.4 12.0 - - - +
284A TYR* 4.1 5.2 - - - -
288A GLN* 5.5 0.7 - - - +
319A SER* 5.4 1.1 - - - -
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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
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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