Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 1L2L
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 THR 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLU* 5.2 1.7 + - - -
62A TYR* 4.9 1.6 + - - -
70A ILE* 3.6 5.8 - - - +
71A GLU* 1.3 95.0 - - + +
73A ILE* 1.3 66.3 + - - +
74A PRO* 3.5 13.1 - - - +
75A GLN* 3.1 39.8 + - - +
76A LEU 3.1 9.5 + - - -
98A GLU* 5.2 5.4 - - - +
99A VAL* 3.4 10.1 - - - -
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Residues in contact with ILE 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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54A VAL* 3.4 27.1 - - + -
72A THR* 1.3 71.6 - - - +
74A PRO* 1.3 70.7 - - + +
76A LEU* 3.0 16.7 + - + +
77A LEU* 3.0 17.1 + - + +
98A GLU* 4.1 23.4 + - + +
99A VAL* 3.7 9.6 - - + +
102A TYR* 3.3 61.9 - - + +
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Residues in contact with PRO 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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54A VAL* 3.9 27.6 - - + +
58A GLU* 4.1 35.0 - - + +
59A VAL* 4.0 17.2 - - + +
62A TYR* 3.6 9.5 - - + -
72A THR* 3.5 14.1 - - - +
73A ILE* 1.3 93.9 - - + +
75A GLN* 1.3 51.3 + - - +
77A LEU* 3.5 0.5 + - - -
78A GLY* 2.8 33.3 + - - -
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Residues in contact with GLN 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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62A TYR* 3.4 47.1 + - + -
67A PRO* 4.0 13.0 - - + +
69A GLU 3.2 12.7 - - - +
70A ILE* 4.3 8.1 - - + -
71A GLU* 2.7 38.7 + - - +
72A THR* 3.1 26.4 + - - +
74A PRO* 1.3 79.3 - - - +
76A LEU* 1.3 54.5 + - - +
79A SER* 2.6 38.6 + - - -
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Residues in contact with LEU 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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70A ILE* 3.7 33.8 - - + +
72A THR 3.1 6.6 + - - +
73A ILE 3.0 8.8 + - - +
75A GLN* 1.3 75.8 - - - +
77A LEU* 1.3 88.7 + - + +
79A SER* 3.1 4.3 + - - -
80A ILE* 3.0 39.9 + - + +
99A VAL* 4.2 7.6 - - + -
102A TYR* 4.2 14.1 - - + -
103A MET* 4.0 33.4 - - + -
106A TRP* 3.7 18.2 - - + -
182A TYR* 4.3 2.5 - - + -
201A PHE* 4.3 4.3 - - + -
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Residues in contact with LEU 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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47A LEU* 4.4 8.8 - - + +
50A ARG* 3.6 38.8 - - + +
51A ILE* 3.7 18.1 - - + +
54A VAL* 3.9 10.1 - - + -
59A VAL* 3.7 14.6 - - + -
73A ILE* 3.0 21.3 + - + +
76A LEU* 1.3 94.8 - - + +
78A GLY* 1.3 63.8 + - - +
80A ILE* 3.1 8.7 + - + +
81A LEU* 3.0 24.8 + - - +
102A TYR* 4.1 10.3 - - - +
106A TRP* 3.7 24.9 - - + -
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Residues in contact with GLY 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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59A VAL* 3.3 31.8 - - - +
62A TYR* 3.8 11.2 - - - -
63A SER* 3.2 11.3 - - - -
74A PRO 2.8 18.8 + - - -
77A LEU* 1.3 73.3 - - - +
79A SER* 1.3 58.0 + - - +
81A LEU* 3.2 2.9 + - - +
82A TRP 2.8 23.6 + - - -
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Residues in contact with SER 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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62A TYR* 4.4 1.3 - - - +
66A LEU* 3.8 12.6 - - - -
67A PRO* 3.3 21.1 - - - +
70A ILE* 4.2 2.8 - - - +
75A GLN 2.6 23.3 + - - -
76A LEU 3.1 5.4 + - - -
78A GLY* 1.3 72.9 - - - +
80A ILE* 1.3 65.6 + - - +
82A TRP* 3.2 10.3 + - - +
83A SER 3.2 10.0 + - - -
92A LEU* 3.6 6.4 - - - +
201A PHE* 3.5 40.6 - - - -
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Residues in contact with ILE 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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42A LEU* 3.7 30.7 - - + -
47A LEU* 4.5 10.1 - - + -
76A LEU* 3.0 22.9 + - + +
77A LEU* 3.1 18.6 + - + +
79A SER* 1.3 76.5 - - - +
81A LEU* 1.3 63.7 + - - +
83A SER* 3.1 6.9 + - - -
84A ILE* 3.0 29.3 + - + +
106A TRP* 5.1 3.4 - - + -
182A TYR* 3.5 30.1 - - + +
184A PHE* 5.5 0.9 - - + -
201A PHE* 3.2 36.3 - - + -
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Residues in contact with LEU 81 (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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47A LEU* 4.5 3.8 - - + -
51A ILE* 3.8 16.4 - - + -
59A VAL* 3.8 21.8 - - + -
60A LEU* 4.4 3.6 - - + -
63A SER* 3.5 13.9 - - - -
77A LEU 3.0 13.8 + - - +
78A GLY 3.2 8.0 + - - +
80A ILE* 1.3 75.3 - - - +
82A TRP* 1.3 65.7 + - - +
84A ILE* 3.6 9.1 - - + +
85A LYS* 2.9 28.4 + - - +
190A VAL* 3.3 41.1 - - + -
191A LEU* 4.0 19.1 - - + -
193A PHE* 4.3 17.3 - - + -
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Residues in contact with TRP 82 (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 TYR 3.9 2.5 - - - +
63A SER* 3.4 31.4 - - - +
64A GLU 3.9 9.0 + - - -
65A GLU* 4.7 0.2 - - - +
66A LEU* 3.3 57.9 - - + +
78A GLY 2.8 13.7 + - - +
79A SER 3.3 10.8 - - - +
80A ILE 3.2 0.2 - - - -
81A LEU* 1.3 78.2 - - - +
83A SER* 1.3 72.0 + - - +
85A LYS* 3.6 12.5 - - - +
86A ARG* 3.6 40.8 + - - +
88A LYS* 4.2 22.2 - - + -
89A ALA 4.4 4.0 - - - -
90A ALA* 3.8 17.7 - - + -
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Residues in contact with SER 83 (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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79A SER 3.2 0.6 + - - -
80A ILE 3.1 9.9 + - - -
82A TRP* 1.3 81.0 - - - +
84A ILE* 1.3 52.8 + - - +
87A GLY* 2.6 32.2 + - - -
88A LYS 3.1 31.2 + - - +
90A ALA* 3.7 11.4 + - - +
184A PHE* 3.5 13.6 - - - -
200A ARG 4.3 1.6 - - - -
201A PHE* 3.5 35.7 - - - +
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Residues in contact with ILE 84 (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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42A LEU* 4.2 4.3 - - + -
47A LEU* 3.9 18.8 - - + -
80A ILE* 3.0 26.2 + - + +
81A LEU* 3.1 10.7 + - + +
83A SER* 1.3 72.5 - - - +
85A LYS* 1.3 66.4 + - - +
86A ARG 2.9 5.4 + - - -
87A GLY* 2.9 9.7 + - - -
184A PHE* 3.7 26.5 - - + -
188A PHE* 3.8 31.6 - - + +
190A VAL* 4.0 21.5 - - + -
193A PHE* 4.9 2.7 - - + -
194A GLU 4.5 1.6 - - - -
195A ALA* 3.2 28.6 - - + +
196A PRO* 3.1 11.6 - - - +
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Residues in contact with LYS 85 (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 SER* 3.2 26.8 + - - +
64A GLU* 4.8 12.9 - - - +
81A LEU 2.9 20.8 + - - +
82A TRP 3.6 7.6 - - - +
84A ILE* 1.3 75.3 - - - +
86A ARG* 1.3 74.3 + - + +
193A PHE* 3.7 51.9 - - + +
194A GLU 4.2 9.7 - - - +
196A PRO* 3.6 11.5 - - - +
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Residues in contact with ARG 86 (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 SER 5.1 1.0 + - - -
64A GLU* 4.5 12.9 + - - +
82A TRP* 3.6 57.7 + - - +
83A SER 3.5 0.8 + - - -
84A ILE 3.0 0.6 - - - -
85A LYS* 1.3 92.4 - - + +
87A GLY* 1.3 65.1 + - - +
88A LYS* 3.3 15.5 + - + +
196A PRO* 3.2 16.7 - - - +
197A ARG* 5.4 0.3 - - - +
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Residues in contact with GLY 87 (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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83A SER 2.6 16.5 + - - -
84A ILE 2.9 6.6 + - - -
86A ARG* 1.3 76.3 - - - +
88A LYS* 1.3 52.3 + - - +
184A PHE* 4.2 2.7 - - - -
196A PRO* 3.4 12.5 - - - +
197A ARG* 3.6 35.1 - - - +
199A ASN* 2.8 26.0 + - - -
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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