Contacts of the helix formed by residues 66 - 85 (chain B) in PDB entry 2X1L
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 PRO 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ALA* 5.6 10.1 - - + -
72A ARG* 5.7 4.3 - - - +
64B GLY 4.7 0.7 - - - +
65B ILE* 1.4 93.0 - - + +
67B ALA* 1.3 66.1 + - - +
68B ALA* 4.5 4.0 - - + +
69B GLU* 3.1 29.9 + - + +
70B LEU* 3.1 12.5 + - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B MET* 4.9 2.2 - - - +
57B ALA* 4.6 7.2 - - + -
60B ALA* 3.6 20.0 - - + +
65B ILE 3.7 1.6 + - - -
66B PRO* 1.3 72.2 - - - +
68B ALA* 1.3 56.7 + - - +
70B LEU* 3.4 4.0 + - - +
71B ALA* 3.0 29.5 + - - +
215B TRP* 3.6 42.4 + - + +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.6 39.7 + - - +
66B PRO* 3.3 3.5 - - + +
67B ALA* 1.3 78.4 - - - +
69B GLU* 1.3 61.2 + - - +
71B ALA* 3.8 2.1 - - - +
72B ARG* 3.2 24.9 + - - +
215B TRP* 3.6 27.2 - - + -
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG* 3.6 18.2 - - - +
94A ARG* 5.1 0.5 + - - -
96A SER* 4.7 14.3 + - - +
97A ASP* 4.6 6.6 - - - +
65B ILE* 4.7 13.2 - - + -
66B PRO* 3.1 29.3 + - + +
68B ALA* 1.3 77.4 - - - +
70B LEU* 1.3 65.2 + - - +
72B ARG* 2.8 44.7 + - - +
73B ARG* 3.1 28.4 + - + +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO 4.7 0.2 - - - +
56B MET* 3.7 42.6 - - + +
59B THR* 4.1 17.5 - - + -
60B ALA* 3.8 18.8 - - + +
63B GLU* 3.6 12.8 - - - +
65B ILE* 3.7 19.2 - - + +
66B PRO 3.1 7.1 + - - +
67B ALA 3.7 5.8 - - - +
69B GLU* 1.3 78.8 - - - +
71B ALA* 1.3 55.8 + - - +
73B ARG* 3.4 32.7 + - - +
74B ASN* 2.9 52.0 + - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 4.4 1.2 - - - +
51B VAL* 3.7 29.6 - - + -
56B MET* 3.9 15.9 - - + +
67B ALA 3.0 18.0 + - - +
68B ALA* 3.8 5.8 - - - +
70B LEU* 1.3 77.1 - - - +
72B ARG* 1.3 56.4 + - - +
75B SER* 2.7 37.7 + - - -
94B ARG* 5.5 0.4 - - - -
96B SER* 5.8 2.5 - - - +
215B TRP* 4.0 10.1 - - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG* 3.8 9.9 - - - +
76A ASP* 3.8 19.3 - - - -
79A GLN* 4.7 7.3 + - - +
94A ARG* 3.4 46.6 - - - +
97A ASP* 4.4 6.5 + - - -
68B ALA 3.2 10.0 + - - +
69B GLU* 2.8 47.9 + - - +
70B LEU 3.4 0.2 - - - -
71B ALA* 1.3 78.8 - - - +
73B ARG* 1.3 67.7 + - - +
76B ASP* 3.2 35.5 + - - +
94B ARG* 3.3 20.0 + - - +
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 6.2 1.6 - - - +
63B GLU* 2.8 40.6 + - - -
65B ILE* 3.6 15.7 - - - +
69B GLU* 3.1 22.7 + - + +
70B LEU* 3.4 12.3 - - - +
72B ARG* 1.3 82.2 - - - +
74B ASN* 1.3 85.9 + - - +
76B ASP* 3.3 22.6 - - - +
77B VAL* 3.4 13.6 - - + +
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 3.0 34.6 + - + +
15B ASN 3.8 16.0 + - - -
16B GLY* 4.0 11.2 + - - +
70B LEU* 2.9 36.0 + - - +
73B ARG* 1.3 98.2 + - - +
75B SER* 1.3 62.9 + - - +
76B ASP 3.3 0.2 - - - -
77B VAL* 3.4 12.8 + - - +
78B PHE* 3.3 26.5 + - - -
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 3.4 12.2 - - - +
49B THR* 2.9 36.0 + - - -
51B VAL* 3.6 5.5 - - - +
71B ALA 2.7 23.6 + - - -
74B ASN* 1.3 73.5 - - - +
76B ASP* 1.3 60.7 + - - +
78B PHE* 3.2 4.0 + - - +
79B GLN* 2.9 29.3 + - - +
92B PHE* 3.9 3.4 - - - -
94B ARG* 3.5 23.3 - - - -
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLN* 5.6 5.6 + - - -
72B ARG* 3.2 23.8 + - - +
73B ARG* 3.3 13.6 - - - +
75B SER* 1.3 78.7 - - - +
77B VAL* 1.3 56.6 + - + +
79B GLN* 3.3 3.1 + - - +
80B ARG* 2.9 50.7 + - + +
94B ARG* 2.8 29.6 + - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 5.2 8.7 - - + -
18B PRO* 3.9 23.7 - - + +
73B ARG* 3.4 19.3 - - + +
74B ASN* 3.5 15.3 - - - +
75B SER 3.2 0.8 - - - -
76B ASP* 1.3 75.1 - - + +
78B PHE* 1.3 60.1 + - - +
80B ARG* 3.5 7.3 + - + +
81B LEU* 3.2 23.3 + - + +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 3.8 19.3 - - + -
13B TYR 4.3 5.6 - - - -
14B PRO* 3.8 21.8 - - + -
16B GLY 3.7 22.0 - - - -
17B VAL 4.5 0.9 - - - -
18B PRO* 3.6 39.3 - - + -
22B HIS* 3.8 18.4 - + - -
26B TYR* 3.6 29.6 - + - -
48B GLY 5.6 0.2 - - - -
49B THR* 4.0 8.5 - - + -
74B ASN 3.3 19.8 + - - -
75B SER 3.2 9.0 + - - +
77B VAL* 1.3 77.6 - - - +
79B GLN* 1.3 60.9 + - - +
81B LEU* 3.5 4.3 + - + +
82B GLN* 3.3 28.2 + - - +
92B PHE* 3.9 13.7 - - + -
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B SER 2.9 14.5 + - - +
76B ASP* 3.7 4.7 - - - +
78B PHE* 1.3 75.4 - - - +
80B ARG* 1.3 80.5 + - - +
82B GLN* 3.4 3.7 + - - +
83B GLU* 3.1 38.8 + - - +
89B PHE* 4.4 10.8 - - + -
92B PHE* 3.3 48.9 + - + +
94B ARG* 2.8 32.6 + - - +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP 5.7 2.8 + - - -
76B ASP* 2.9 43.2 + - + +
77B VAL* 3.9 7.4 - - + +
78B PHE 3.4 0.2 - - - -
79B GLN* 1.3 91.8 - - - +
81B LEU* 1.3 57.8 + - - +
83B GLU* 2.8 44.1 + - - +
84B LYS* 3.0 27.8 + - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PRO* 3.5 31.4 - - + -
23B ALA* 4.8 5.6 - - + +
26B TYR* 4.8 13.7 - - + -
77B VAL* 3.2 17.8 + - + +
78B PHE* 3.7 5.6 - - - +
79B GLN 3.3 0.2 - - - -
80B ARG* 1.3 74.2 - - - +
82B GLN* 1.3 54.9 + - - +
84B LYS* 3.0 11.2 + - + +
85B LEU* 2.7 61.4 + - + +
312B PRO* 3.8 25.6 - - + -
313B VAL* 3.8 31.0 - - + +
316B VAL* 6.2 0.4 - - + -
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 3.5 44.4 + - + +
45B TYR* 4.7 0.2 + - - -
47B THR* 3.0 40.2 + - - +
48B GLY* 4.4 1.2 + - - +
78B PHE* 3.3 14.2 + - - +
79B GLN* 3.4 6.2 + - - +
81B LEU* 1.3 76.5 - - + +
83B GLU* 1.3 59.8 + - - +
85B LEU* 4.3 2.5 - - - -
86B ASN 3.2 2.6 + - - -
87B ILE* 2.9 63.0 + - + +
89B PHE* 3.8 15.9 - - + -
92B PHE* 3.5 14.2 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLN* 3.1 24.6 + - - +
80B ARG* 2.8 52.3 + - - +
82B GLN* 1.3 78.1 - - - +
84B LYS* 1.3 59.9 + - - +
86B ASN* 3.3 12.8 + - - -
87B ILE 5.0 2.0 - - - +
89B PHE* 4.5 15.4 - - + -
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG 3.0 13.3 + - - +
81B LEU* 3.0 15.4 + - + +
83B GLU* 1.3 75.6 - - - +
85B LEU* 1.3 59.8 + - + +
86B ASN 3.2 2.8 + - - -
313B VAL* 4.2 30.3 + - + -
316B VAL* 3.8 24.9 - - + +
317B ASP* 2.8 32.7 + - - -
321B LEU* 3.6 17.8 - - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 3.8 38.1 - - + +
26B TYR* 4.4 13.0 - - + -
27B ILE* 4.0 19.1 - - + -
81B LEU* 2.7 45.1 + - + +
82B GLN* 4.5 1.1 - - - -
83B GLU 3.3 0.4 - - - -
84B LYS* 1.3 72.9 - - + +
86B ASN* 1.3 62.6 + - - +
87B ILE* 3.5 13.8 + - + +
312B PRO* 5.1 1.8 - - + -
316B VAL* 3.9 27.4 - - + -
321B LEU* 3.6 15.9 - - + +
324B VAL* 5.7 1.3 - - + -
325B ARG* 3.0 24.8 + - - -
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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