Contacts of the helix formed by residues 65 - 80 (chain A) in PDB entry 1LL9
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 VAL 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.5 17.7 - - + +
63A GLY 3.0 1.4 + - - -
64A SER* 1.3 77.0 - - - +
66A SER* 1.3 59.0 + - - +
67A LYS 3.0 0.2 - - - -
68A THR* 2.7 41.0 + - + +
69A PHE* 3.9 2.6 - - + -
230A MET* 3.9 28.0 - - + -
233A TRP* 5.3 0.7 - - - +
271A TRP* 5.6 0.2 - - + -
315A LYS* 3.7 31.6 - - + +
316A THR 3.9 0.7 - - - -
317A GLY* 3.9 8.2 - - - +
324A SER* 3.2 28.0 - - - +
326A VAL* 4.0 13.5 - - + -
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.0 3.2 - - - +
63A GLY 2.7 20.5 + - - -
64A SER 2.8 0.2 - - - -
65A VAL* 1.3 78.5 - - - +
67A LYS* 1.3 62.3 + - - +
69A PHE* 2.9 27.3 + - - +
70A THR* 3.1 13.2 + - - -
218A ALA 4.8 4.0 - - - -
219A GLU 4.8 0.4 - - - -
220A ALA 4.1 2.9 - - - -
221A TYR* 3.5 14.8 - - - -
222A GLY 3.9 1.8 - - - -
223A VAL* 2.9 43.6 + - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 2.9 28.8 + - - +
66A SER* 1.3 78.4 - - - +
68A THR* 1.3 56.2 + - - +
70A THR* 3.3 9.2 + - - -
71A GLY* 2.8 24.6 + - - -
112A TYR* 3.2 23.6 - - - +
150A TYR* 3.4 21.5 + - - +
151A ALA 4.5 0.4 - - - -
152A ASN* 2.5 32.4 + - - +
155A ILE* 3.3 34.4 - - + +
219A GLU 4.6 0.4 - - - +
220A ALA* 2.9 29.4 + - - +
270A GLY* 3.6 18.2 - - - -
315A LYS* 4.1 4.7 - - - -
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Residues in contact with THR 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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65A VAL* 2.7 23.6 + - + +
67A LYS* 1.3 78.4 - - - +
69A PHE* 1.3 63.5 + - - +
71A GLY* 3.4 0.7 + - - -
72A VAL* 3.1 28.8 + - - +
233A TRP* 3.1 21.9 + - - -
269A LEU 4.6 2.4 - - - +
270A GLY* 4.2 6.7 - - - -
271A TRP* 3.5 56.9 + - + +
315A LYS* 3.7 18.8 - - + -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.8 23.8 - - + -
65A VAL 3.9 7.9 - - - -
66A SER* 2.9 14.3 + - - +
68A THR* 1.3 86.0 + - - +
70A THR* 1.3 59.2 + - - +
72A VAL* 3.2 2.1 + - - +
73A LEU* 2.8 31.0 + - - +
174A MET* 3.6 21.1 - - + +
178A VAL* 4.2 6.1 - - + +
179A PHE* 3.7 21.5 - + + -
184A LEU* 3.9 16.6 - - + -
187A THR* 4.7 7.2 - - + -
223A VAL* 4.4 11.2 - - + -
230A MET* 4.0 11.4 - - + -
233A TRP* 3.3 63.0 - + + -
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER 3.1 9.4 + - - -
67A LYS* 3.6 9.2 - - - -
69A PHE* 1.3 76.5 - - - +
71A GLY* 1.3 56.8 + - - +
73A LEU* 3.3 3.3 + - - +
74A GLY* 2.9 26.5 + - - -
155A ILE* 4.2 19.7 - - + +
158A PHE* 4.2 2.9 - - + -
159A GLY* 3.7 30.7 - - - +
170A PHE* 3.5 14.2 - - + -
174A MET* 3.8 8.7 - - - +
218A ALA 4.5 1.0 + - - -
219A GLU* 2.6 31.2 + - - +
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Residues in contact with GLY 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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67A LYS 2.8 12.7 + - - -
68A THR 3.4 0.4 + - - -
69A PHE 3.2 0.2 - - - -
70A THR* 1.3 78.1 - - - +
72A VAL* 1.3 55.8 + - - +
74A GLY* 3.3 1.9 + - - -
75A GLY* 2.9 24.1 + - - -
155A ILE* 5.3 3.5 - - - +
158A PHE* 4.9 6.0 - - - -
255A ALA* 4.1 7.2 - - - +
269A LEU* 3.5 40.1 - - - +
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Residues in contact with VAL 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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68A THR 3.1 17.7 + - - +
69A PHE 3.2 2.0 + - - +
71A GLY* 1.3 74.0 - - - +
73A LEU* 1.3 60.5 - - - +
75A GLY* 3.1 1.1 + - - +
76A ASP* 2.8 27.7 + - - +
178A VAL* 4.7 4.3 - - + -
233A TRP* 3.5 27.6 - - + -
237A ASN* 4.2 12.1 - - - +
248A LEU* 3.8 19.1 - - + -
251A GLY* 4.2 6.6 - - - -
252A ILE* 3.6 31.4 - - + +
255A ALA* 3.9 17.3 - - + -
271A TRP* 4.5 2.0 - - - +
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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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69A PHE 2.8 17.2 + - - +
70A THR 3.7 3.6 - - - +
72A VAL* 1.3 76.6 - - - +
74A GLY* 1.3 63.4 + - - +
76A ASP* 3.2 5.7 + - - +
77A ALA* 3.0 22.1 + - + +
162A ALA* 5.7 1.3 - - + -
163A VAL* 3.9 20.0 - - + -
170A PHE* 3.6 31.9 - - + +
173A ALA* 3.8 28.5 - - + +
174A MET* 3.7 26.7 - - + +
177A ARG* 4.1 15.2 + - + +
178A VAL* 3.9 19.0 - - + +
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Residues in contact with GLY 74 (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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70A THR 2.9 14.9 + - - -
71A GLY 3.7 3.6 - - - -
73A LEU* 1.3 78.4 - - - +
75A GLY* 1.3 60.5 + - - +
77A ALA* 3.1 5.3 + - - +
78A ILE* 3.0 29.8 + - - +
83A ILE* 4.0 1.2 - - - +
158A PHE* 3.9 21.8 - - - -
162A ALA* 4.3 13.5 - - - -
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Residues in contact with GLY 75 (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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71A GLY 2.9 15.4 + - - -
72A VAL 3.1 3.3 + - - -
74A GLY* 1.3 75.0 - - - +
76A ASP* 1.3 57.2 + - - +
78A ILE* 3.2 16.7 + - - +
79A ALA* 3.0 24.6 + - - +
251A GLY* 3.4 24.1 - - - -
254A LEU* 3.7 10.2 - - - +
269A LEU* 4.5 2.8 - - - +
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Residues in contact with ASP 76 (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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72A VAL 2.8 12.2 + - - +
73A LEU* 3.5 13.4 - - + +
74A GLY 3.2 0.2 - - - -
75A GLY* 1.3 73.6 - - - +
77A ALA* 1.3 61.6 + - - +
79A ALA* 3.2 2.8 + - - +
80A ARG* 2.6 56.6 + - - +
177A ARG* 3.5 22.7 + - - +
178A VAL* 5.5 0.4 - - + -
247A THR* 2.8 35.2 + - - +
248A LEU* 3.2 26.3 + - + +
251A GLY* 3.5 1.2 - - - -
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Residues in contact with ALA 77 (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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73A LEU 3.0 12.5 + - - +
74A GLY* 3.1 10.7 + - - +
76A ASP* 1.3 78.5 + - - +
78A ILE* 1.3 62.5 + - - +
80A ARG* 3.3 4.3 + - - +
81A GLY 3.1 3.3 + - - -
82A GLU* 3.0 44.2 + - + +
83A ILE* 3.6 13.2 + - + -
162A ALA* 3.9 23.3 - - + +
163A VAL* 5.9 1.1 - - + -
177A ARG* 4.7 3.6 - - - +
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Residues in contact with ILE 78 (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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74A GLY 3.0 18.2 + - - +
75A GLY* 3.4 15.0 - - - +
76A ASP 3.2 0.2 - - - -
77A ALA* 1.3 76.6 - - - +
79A ALA* 1.3 57.8 + - - +
81A GLY* 2.8 21.1 + - - -
83A ILE* 3.5 31.3 - - + +
84A LYS* 5.0 4.0 - - - -
85A LEU* 3.4 44.0 - - + +
254A LEU* 3.8 10.1 - - + -
269A LEU* 4.5 5.4 - - + -
305B THR* 5.8 1.8 - - + +
306B PRO* 3.7 36.0 - - + +
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Residues in contact with ALA 79 (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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75A GLY 3.0 12.0 + - - +
76A ASP 3.5 5.4 - - - +
78A ILE* 1.3 78.8 - - - +
80A ARG* 1.3 60.1 + - - +
81A GLY* 3.1 0.9 + - - -
247A THR* 3.5 36.3 - - - +
250A GLN* 3.5 36.2 + - + +
254A LEU* 5.0 2.7 - - + -
306B PRO* 5.5 4.3 - - - -
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Residues in contact with ARG 80 (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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76A ASP* 2.6 40.6 + - - +
77A ALA 3.6 5.8 - - - +
78A ILE 3.1 0.4 - - - -
79A ALA* 1.3 76.1 - - - +
81A GLY* 1.3 61.3 + - - +
82A GLU* 3.5 16.5 + - + +
176A THR 5.7 0.2 + - - -
177A ARG* 3.2 57.6 + - - +
247A THR* 3.6 26.9 + - + +
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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
------------------------------------------------------------
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