Contacts of the helix formed by residues 62 - 75 (chain B) in PDB entry 5TXV
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ILE* 5.4 5.4 - - - -
60B GLY* 3.3 4.8 + - - -
61B VAL* 1.3 81.9 - - - +
63B LYS* 1.3 65.7 + - - +
64B THR 3.3 2.7 - - - -
65B GLU* 3.8 16.6 - - - +
66B ILE* 3.1 30.5 + - - +
332B LEU* 4.3 3.6 - - - -
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Residues in contact with LYS 63 (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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55B MET* 3.2 55.6 - - + +
56B ILE 4.2 3.6 - - - +
57B GLY* 3.6 17.2 + - - +
58B PRO 3.0 28.9 + - - -
59B THR* 3.8 9.1 - - - +
60B GLY 4.3 3.0 - - - +
61B VAL* 3.7 6.6 - - + +
62B GLY* 1.3 77.2 - - - +
64B THR* 1.3 63.9 + - - +
66B ILE 3.4 0.7 + - - -
67B ALA 3.4 12.0 + - - -
254B PHE* 3.7 9.6 - - + -
256B ASP* 5.0 4.3 - - - -
307B SER* 3.8 20.0 - - - -
308B GLY* 4.6 5.8 - - - +
332B LEU* 3.6 27.3 - - + +
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Residues in contact with THR 64 (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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62B GLY 3.3 0.4 - - - -
63B LYS* 1.3 75.5 - - - +
65B GLU* 1.3 55.5 + - - +
67B ALA* 3.0 3.3 + - - +
68B ARG* 2.7 57.3 + - + +
78B PHE* 4.9 2.2 - - + -
80B LYS* 3.4 38.7 + - + +
254B PHE* 3.4 30.6 - - + -
256B ASP* 5.1 1.4 + - - -
286C GLU* 6.0 0.7 - - - -
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Residues in contact with GLU 65 (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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16B HIS* 5.3 1.0 - - - +
17B ILE* 4.0 15.3 - - + +
62B GLY* 3.3 17.9 + - - +
64B THR* 1.3 79.5 - - - +
66B ILE* 1.3 57.3 + - - +
68B ARG* 4.1 18.7 - - - +
69B ARG* 2.7 74.3 + - - +
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Residues in contact with ILE 66 (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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13B LEU* 4.5 9.2 - - + +
17B ILE* 3.9 27.1 - - + -
20B GLN* 4.4 12.6 - - + +
23B ALA* 3.5 32.5 - - + +
24B LYS* 4.6 4.3 - - + +
27B VAL* 3.7 41.1 - - + -
55B MET* 3.8 4.5 - - + -
62B GLY 3.1 16.8 + - - +
63B LYS 3.6 6.7 - - - +
64B THR 3.2 0.2 - - - -
65B GLU* 1.3 77.0 - - - +
67B ALA* 1.3 56.3 + - - +
69B ARG* 4.3 0.3 - - - +
70B LEU* 2.8 32.9 + - - +
332B LEU* 3.9 12.1 - - + -
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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
----------------------------------------------------------
55B MET* 4.6 0.6 - - - +
63B LYS 3.4 2.2 + - - +
64B THR 3.0 6.5 + - - +
66B ILE* 1.3 79.3 - - - +
68B ARG* 1.3 63.0 + - - +
70B LEU* 3.7 4.4 - - - +
71B ALA* 3.1 24.9 + - - +
78B PHE* 3.6 18.5 - - + -
252B ILE* 5.0 1.0 - - - +
254B PHE* 3.4 35.4 - - + -
305B ILE* 3.7 22.9 - - + -
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Residues in contact with ARG 68 (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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64B THR* 2.7 36.1 + - + +
65B GLU* 3.7 24.5 - - - +
67B ALA* 1.3 74.7 - - - +
69B ARG* 1.3 60.6 + - + +
71B ALA* 3.4 2.1 + - - +
72B LYS* 2.9 35.4 + - - +
78B PHE* 3.8 35.2 - - + -
80B LYS* 4.5 19.8 - - - +
286C GLU* 3.8 31.1 + - - +
287C GLY 3.9 13.7 + - - -
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Residues in contact with ARG 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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13B LEU* 3.8 20.3 - - + +
16B HIS* 3.3 37.7 + - + +
17B ILE* 3.7 14.8 - - + -
65B GLU* 2.7 48.8 + - - +
68B ARG* 1.3 74.4 - - - +
70B LEU* 1.3 52.2 + - - +
72B LYS* 3.8 32.8 - - - +
73B LEU* 2.6 36.4 + - - +
47C GLU* 2.4 47.1 + - - -
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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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9B ILE* 4.2 14.6 - - + -
13B LEU* 4.2 6.7 - - + +
27B VAL* 3.9 46.4 - - + +
31B LEU* 4.1 27.1 - - + +
66B ILE 2.8 20.1 + - - +
67B ALA* 3.7 3.8 - - - +
69B ARG* 1.3 77.6 - - - +
71B ALA* 1.3 56.8 + - - +
73B LEU* 3.2 7.8 + - + +
74B ALA* 3.0 27.5 + - - +
252B ILE* 4.6 15.3 - - + -
303B LEU* 4.7 11.4 - - + -
305B ILE* 4.4 19.5 - - + -
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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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67B ALA 3.1 16.2 + - - +
68B ARG 3.9 1.8 - - - +
70B LEU* 1.3 76.1 - - - +
72B LYS* 1.3 58.7 + - - +
74B ALA 3.1 0.7 + - - -
75B ASN* 2.8 26.2 + - - -
76B ALA* 2.9 20.2 + - - +
78B PHE* 3.5 32.5 - - + -
252B ILE* 3.6 24.7 - - + +
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Residues in contact with LYS 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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16B HIS* 6.2 0.2 - - - +
68B ARG* 2.9 22.4 + - - +
69B ARG* 3.8 36.6 - - - +
71B ALA* 1.3 76.5 - - - +
73B LEU* 1.3 61.9 + - - +
75B ASN* 3.4 11.7 + - - +
46C HIS* 6.3 1.0 - - - +
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Residues in contact with LEU 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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4B MET* 3.7 35.3 - - + +
9B ILE* 3.8 39.9 - - + +
12B GLU* 3.8 32.1 - - + -
13B LEU* 5.1 7.0 - - + -
31B LEU* 4.7 6.7 - - + -
69B ARG 2.6 22.2 + - - +
70B LEU* 3.4 6.5 - - + +
71B ALA 3.2 0.2 - - - -
72B LYS* 1.3 75.7 - - - +
74B ALA* 1.3 60.0 + - - +
75B ASN* 3.6 1.2 + - - +
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Residues in contact with ALA 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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4B MET* 5.8 1.8 - - - -
31B LEU* 4.0 29.8 - - + -
34B ARG* 6.1 0.4 - - - +
70B LEU 3.0 15.3 + - - +
71B ALA* 3.9 3.6 - - - +
73B LEU* 1.3 76.3 - - - +
75B ASN* 1.3 68.2 + - - +
76B ALA* 3.2 15.1 + - + +
250B HIS* 5.5 7.5 - - + -
252B ILE* 5.2 1.3 - - + -
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Residues in contact with ASN 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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71B ALA 2.8 6.5 + - - -
72B LYS* 3.4 9.0 + - - +
73B LEU 3.3 4.4 - - - +
74B ALA* 1.3 78.5 - - - +
76B ALA* 1.3 61.8 + - - +
77B PRO* 4.1 2.1 - - - +
246B ALA* 5.9 1.0 - - - +
250B HIS* 6.0 1.5 - - - -
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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