Contacts of the helix formed by residues 62 - 83 (chain L) in PDB entry 3V3K
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 LEU 62 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ILE* 4.3 1.8 - - + +
53L TYR* 4.1 45.3 - - + +
56L ALA* 3.7 26.2 - - + -
57L ARG 5.2 4.7 - - - +
58L ASN 3.7 16.4 - - - +
59L ASN* 3.3 16.2 + - - +
61L GLU* 1.3 73.2 - - - +
63L GLU* 1.3 59.3 + - - +
64L GLU 3.3 3.6 - - - -
65L ILE* 3.0 19.0 + - + +
66L PHE* 3.0 27.1 + - - +
136L CYS* 4.9 9.6 - - - -
138L VAL* 4.5 10.4 - - + +
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Residues in contact with GLU 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L ASN* 3.6 21.8 + - - +
60L ASN* 3.7 24.5 - - - +
61L GLU 3.3 1.8 - - - -
62L LEU* 1.3 75.9 - - - +
64L GLU* 1.3 61.7 + - + +
66L PHE* 3.6 17.5 + - - +
67L GLN* 3.4 31.1 + - - +
137L LYS* 4.3 23.3 + - - +
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Residues in contact with GLU 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L ASN 6.0 0.9 - - - +
61L GLU 4.1 11.4 + - - +
62L LEU 3.3 0.8 - - - -
63L GLU* 1.3 77.8 - - + +
65L ILE* 1.3 66.8 + - + +
66L PHE 3.7 0.2 + - - -
67L GLN* 3.8 14.9 + - - +
68L GLU* 3.4 22.7 + - - +
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Residues in contact with ILE 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L MET* 3.7 34.8 - - + +
52L ILE* 3.4 52.9 - - + -
53L TYR* 5.3 6.3 - - + +
61L GLU 5.1 1.6 - - - +
62L LEU* 3.0 20.5 + - + +
64L GLU* 1.3 78.6 - - + +
66L PHE* 1.3 64.9 + - - +
68L GLU* 3.3 33.4 + - - +
69L LEU* 3.5 9.5 + - + +
138L VAL* 4.6 21.8 - - + -
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Residues in contact with PHE 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L LEU 3.0 12.7 + - - +
63L GLU* 3.7 22.9 - - - +
64L GLU 3.4 0.4 - - - -
65L ILE* 1.3 77.0 - - - +
67L GLN* 1.3 66.0 + - + +
68L GLU 3.3 0.2 + - - -
69L LEU* 3.4 3.9 + - - +
70L SER* 3.1 38.3 + - - -
137L LYS* 3.5 45.3 - - + -
138L VAL* 4.2 10.5 - - + +
141L LEU* 3.5 38.6 - - + -
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Residues in contact with GLN 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L GLU* 3.4 17.8 + - - +
64L GLU* 4.1 10.9 - - - +
65L ILE 3.3 0.6 - - - -
66L PHE* 1.3 81.4 - - + +
68L GLU* 1.3 60.4 + - + +
70L SER* 3.5 9.0 + - - +
71L ALA* 3.2 23.4 + - - +
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Residues in contact with GLU 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L LYS* 4.2 16.7 + - - +
48L VAL* 5.9 3.7 - - - +
49L MET* 3.3 37.6 - - + +
52L ILE* 5.6 0.5 - - - +
64L GLU* 3.4 19.3 + - - +
65L ILE* 3.3 25.3 + - - +
66L PHE 3.2 0.6 - - - -
67L GLN* 1.3 76.3 - - - +
69L LEU* 1.3 55.6 + - - +
71L ALA* 3.4 4.3 + - - +
72L PHE* 2.8 37.2 + - - +
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Residues in contact with LEU 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L MET* 4.7 10.5 - - + -
65L ILE* 3.5 8.4 + - + +
66L PHE 3.4 3.6 + - - +
68L GLU* 1.3 79.1 - - - +
70L SER* 1.3 54.2 + - - +
72L PHE* 4.3 5.4 - - + -
73L VAL* 2.7 42.9 + - + +
116L PHE* 4.9 5.8 - - + -
117L LEU* 3.9 28.3 - - + -
120L LEU* 4.3 19.7 - - + -
138L VAL* 3.4 44.2 - - + +
141L LEU* 3.5 22.9 - - + -
142L LEU* 4.2 12.6 - - + -
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Residues in contact with SER 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K GLU* 4.9 2.6 + - - -
66L PHE* 3.1 33.8 + - - -
67L GLN* 3.5 12.3 + - - +
69L LEU* 1.3 77.8 - - - +
71L ALA* 1.3 59.3 + - - +
73L VAL* 4.7 4.0 - - - +
74L SER* 2.9 26.4 + - - -
141L LEU* 4.1 14.5 - - - +
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Residues in contact with ALA 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L GLN 3.2 18.3 + - - +
68L GLU* 3.6 4.5 - - - +
69L LEU 3.2 0.2 - - - -
70L SER* 1.3 79.6 + - - +
72L PHE* 1.3 58.8 + - - +
74L SER* 2.7 18.5 + - - -
75L GLY* 3.0 13.2 + - - -
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Residues in contact with PHE 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L LEU* 4.8 11.0 - - + -
45L LYS* 4.2 24.0 - - + +
68L GLU 2.8 22.9 + - - +
69L LEU* 3.7 6.1 - - + +
71L ALA* 1.3 74.7 - - - +
73L VAL* 1.3 53.1 + - + +
75L GLY* 3.4 1.7 + - - -
76L LEU* 2.7 38.9 + - + +
113L ASP* 3.7 50.5 - - + -
116L PHE* 3.5 38.6 - + + -
117L LEU* 4.2 19.5 - - + -
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Residues in contact with VAL 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L LEU* 2.7 32.8 + - + +
70L SER* 4.7 3.4 - - - +
72L PHE* 1.3 69.2 - - - +
74L SER* 1.3 61.0 + - - +
76L LEU* 3.6 8.5 - - + +
77L MET* 2.8 40.8 + - + +
117L LEU* 3.9 32.1 - - + -
141L LEU* 4.9 19.1 - - + +
150L LEU* 4.2 22.2 - - + -
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Residues in contact with SER 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K GLU* 4.0 31.0 + - - +
70L SER 2.9 18.3 + - - -
71L ALA* 2.7 23.9 + - - -
73L VAL* 1.3 78.4 - - - +
75L GLY* 1.3 55.9 + - - +
77L MET* 3.6 10.7 + - - +
78L ASP* 3.0 34.1 + - - +
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Residues in contact with GLY 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L ALA 3.0 15.2 + - - -
72L PHE* 3.7 3.1 - - - -
74L SER* 1.3 75.6 + - - +
76L LEU* 1.3 53.3 + - - +
78L ASP* 3.2 10.0 + - - +
79L LYS* 2.8 35.2 + - - +
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Residues in contact with LEU 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L PHE* 2.7 27.1 + - + +
73L VAL* 3.6 11.0 - - + +
75L GLY* 1.3 72.7 - - - +
77L MET* 1.3 66.0 + - + +
79L LYS* 3.4 6.9 + - + +
80L ARG* 3.2 17.7 + - + -
110L TYR* 3.3 48.6 - - + +
113L ASP* 3.6 33.9 - - + +
114L LEU* 4.4 2.7 - - + +
117L LEU* 4.3 15.5 - - + -
150L LEU* 3.9 24.5 - - + -
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Residues in contact with MET 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K ARG* 3.2 76.5 - - - +
73L VAL* 2.8 29.3 + - + +
74L SER* 3.7 9.0 - - - +
75L GLY 3.2 0.2 - - - -
76L LEU* 1.3 79.3 - - + +
78L ASP* 1.3 62.8 + - - +
80L ARG* 3.5 6.5 + - - +
81L ASN* 3.1 32.3 + - - +
149L GLU* 4.6 14.9 - - + +
150L LEU* 6.2 5.2 - - + -
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Residues in contact with ASP 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K ARG* 2.9 36.0 + - - -
74L SER* 3.0 22.5 + - - +
75L GLY* 3.5 10.6 - - - +
77L MET* 1.3 74.1 - - - +
79L LYS* 1.3 62.9 + - - +
81L ASN* 3.5 9.2 + - - +
82L SER* 3.3 22.9 + - - -
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Residues in contact with LYS 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L GLY 2.8 20.6 + - - +
76L LEU* 3.5 11.7 - - + +
77L MET 3.3 0.4 - - - -
78L ASP* 1.3 72.7 - - - +
80L ARG* 1.3 60.3 + - - +
82L SER* 2.8 20.6 + - - +
83L VAL* 3.1 29.6 - - + +
106L ASP 4.9 0.7 - - - -
109L SER* 3.0 46.3 + - - -
110L TYR* 3.9 15.0 - - + +
113L ASP* 2.9 29.4 + - - +
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Residues in contact with ARG 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L LEU* 3.2 7.6 + - + +
77L MET* 3.8 10.3 - - - +
78L ASP 3.3 0.2 - - - -
79L LYS* 1.3 77.9 - - - +
81L ASN* 1.3 59.2 + - - +
84L PHE* 2.8 50.8 + - + +
86L VAL* 5.1 3.4 - - - +
110L TYR* 3.5 31.2 + - + -
149L GLU* 3.3 46.2 + - - +
153L ASP* 2.9 34.1 + - - -
178L ASP 3.5 17.3 + - - -
179L LEU* 3.6 30.9 + - - +
181L TYR 5.9 0.6 + - - -
183L LYS* 4.0 14.6 - - - +
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Residues in contact with ASN 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K ARG* 4.6 17.0 - - - +
77L MET* 3.1 28.2 + - - +
78L ASP* 3.5 10.2 + - - +
79L LYS 3.4 0.4 - - - -
80L ARG* 1.3 77.9 - - - +
82L SER* 1.3 58.5 + - - +
84L PHE 3.4 3.6 - - - +
99L ARG* 3.0 33.6 + - - +
149L GLU* 4.3 17.9 + - - +
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L ASP 3.3 14.2 + - - -
79L LYS* 2.8 25.5 + - - +
81L ASN* 1.3 76.2 - - - +
83L VAL* 1.3 67.2 + - - +
99L ARG* 3.4 24.3 - - - +
102L MET* 4.2 14.9 - - - +
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Residues in contact with VAL 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L LYS* 3.1 29.2 + - + +
82L SER* 1.3 84.0 + - - +
84L PHE* 1.3 89.6 + - + +
98L LEU* 3.8 15.1 - - + -
99L ARG* 2.9 25.3 + - - +
102L MET* 3.4 30.5 - - + +
106L ASP* 3.9 31.2 - - + +
109L SER* 5.4 0.2 - - - +
110L TYR* 5.2 0.9 - - + -
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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