Contacts of the helix formed by residues 71 - 88 (chain I) in PDB entry 3UF2
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 71 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LYS* 4.2 6.1 - - + -
67I PHE* 4.1 4.0 - - - +
68I ARG* 2.9 36.4 + - + +
69I ASP 3.6 7.2 - - - +
70I ASN* 1.3 79.7 - - - +
72I PRO* 1.3 77.8 - - + +
73I ASN* 3.8 3.3 + - - +
74I ALA* 2.9 22.7 + - - +
75I ILE* 3.0 12.7 + - - +
24J ASP* 3.7 41.6 + - + +
25J SER* 5.6 0.2 - - - -
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Residues in contact with PRO 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LYS* 3.8 22.6 - - + -
71I THR* 1.3 88.2 - - - +
73I ASN* 1.3 62.5 + - - +
75I ILE* 3.5 12.9 + - + +
76I ALA* 3.0 26.4 + - - +
24J ASP* 5.6 3.6 - - + -
25J SER* 6.3 2.2 - - - -
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Residues in contact with ASN 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I SER 5.2 0.3 - - - +
21I ARG* 4.6 1.4 - - - +
22I LEU* 3.7 25.8 + - + +
25I SER* 3.5 10.1 + - - -
26I GLN* 4.0 0.4 - - - +
67I PHE* 3.5 28.3 - - + -
71I THR* 3.1 4.2 - - - +
72I PRO* 1.3 79.3 - - - +
74I ALA* 1.3 66.8 + - - +
76I ALA* 2.8 19.1 + - - +
77I ILE* 3.0 15.9 + - - +
25J SER* 2.6 50.2 + - - +
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I PHE* 3.8 21.4 - - - +
68I ARG 3.4 24.5 - - - +
69I ASP* 4.5 2.0 - - - +
70I ASN* 4.0 7.9 - - - +
71I THR* 2.9 15.3 + - - +
73I ASN* 1.3 79.2 - - - +
75I ILE* 1.3 63.2 + - - +
77I ILE* 3.2 12.2 + - - +
78I VAL* 3.3 17.8 + - - +
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Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E THR* 4.9 18.6 - - + -
36E GLU* 3.5 42.0 - - + +
100E LYS* 4.3 6.7 - - - +
105E THR* 4.7 7.6 - - + +
70I ASN* 4.7 4.3 - - - -
71I THR 3.0 15.4 + - - +
72I PRO* 3.7 10.5 - - + +
74I ALA* 1.3 74.6 - - + +
76I ALA* 1.3 63.8 + - - +
78I VAL* 3.2 9.0 + - + +
79I GLN* 3.0 42.1 + - + +
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I SER* 4.0 34.3 + - - +
22I LEU* 4.6 7.0 - - + -
72I PRO 3.0 14.8 + - - +
73I ASN* 2.8 17.1 + - - +
75I ILE* 1.3 77.4 - - - +
77I ILE* 1.3 59.2 + - - +
79I GLN* 3.3 15.9 - - - +
80I LEU* 3.1 29.1 + - + +
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Residues in contact with ILE 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LEU* 3.5 19.3 - - + -
61I MET* 3.9 26.0 - - + +
65I MET* 3.4 35.9 - - + +
67I PHE* 3.4 27.1 - - + -
73I ASN 3.0 12.7 + - - +
74I ALA* 3.2 6.9 + - - +
76I ALA* 1.3 72.9 - - - +
78I VAL* 1.3 55.7 + - + +
80I LEU* 3.0 16.0 + - + +
81I GLN* 2.7 51.7 + - + +
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Residues in contact with VAL 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU* 4.7 29.4 - - + +
86D ARG* 5.8 1.3 - - - +
34E THR* 5.1 15.0 - - + +
74I ALA 3.3 12.5 + - - +
75I ILE* 3.2 10.9 + - + +
77I ILE* 1.3 76.8 - - + +
79I GLN* 1.3 65.6 + - + +
81I GLN* 2.8 18.9 + - - +
82I GLU* 2.7 30.9 + - + +
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Residues in contact with GLN 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E THR* 6.4 1.8 - - - -
14I GLY 5.1 2.1 - - - +
15I HIS* 4.0 28.5 + - + +
18I SER* 4.3 14.0 + - - +
75I ILE* 3.0 38.9 + - + +
76I ALA* 3.3 12.9 - - - +
78I VAL* 1.3 75.9 - - + +
80I LEU* 1.3 53.1 - - + +
82I GLU* 3.3 5.0 + - - +
83I LEU* 2.8 36.4 + - - +
86I ARG* 4.7 2.6 + - - +
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I HIS* 4.1 30.7 - - + +
16I LEU* 6.1 0.2 - - + -
18I SER* 5.0 2.0 - - - +
19I LEU* 3.7 46.2 - - + -
22I LEU* 5.5 0.4 - - + -
61I MET* 3.8 19.3 - - - -
65I MET* 5.4 0.9 - - + -
76I ALA* 3.1 18.6 + - + +
77I ILE* 3.0 25.4 + - + +
79I GLN* 1.3 75.8 - - + +
81I GLN* 1.3 57.6 + - - +
83I LEU* 3.5 6.7 - - + +
84I SER* 3.0 33.6 + - - -
117I VAL* 5.9 0.2 - - + -
121I PHE* 4.3 17.6 - - + -
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Residues in contact with GLN 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LEU* 3.8 28.3 - - + +
58I GLN* 4.2 7.7 + - - +
61I MET* 3.9 25.8 - - + +
62I GLU* 3.7 44.4 + - - +
77I ILE* 2.7 37.8 + - + +
78I VAL* 3.3 20.1 - - - +
80I LEU* 1.3 73.8 - - - +
82I GLU* 1.3 59.8 + - - +
84I SER* 3.6 4.9 + - - -
85I LEU* 3.4 22.3 + - - +
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Residues in contact with GLU 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLU* 3.8 46.8 - - + +
85D LEU* 3.6 14.9 - - + +
32E GLN 5.0 4.2 - - - +
34E THR* 5.0 4.2 + - - -
107E TYR* 4.2 16.8 + - - -
30F SER* 5.2 8.7 + - - +
78I VAL* 2.7 24.8 + - - +
79I GLN* 3.9 4.7 - - - +
81I GLN* 1.3 69.4 - - - +
83I LEU* 1.3 66.5 + - - +
84I SER 3.1 1.8 - - - -
85I LEU* 3.0 14.4 + - - +
86I ARG* 3.1 29.6 + - - +
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Residues in contact with LEU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I MET* 3.8 30.1 - - + +
11I ILE* 4.1 16.2 - - + +
15I HIS* 3.9 29.4 - - + +
79I GLN 2.8 19.2 + - - +
80I LEU* 3.5 7.0 - - + +
82I GLU* 1.3 77.1 - - - +
84I SER* 1.3 56.3 + - - +
86I ARG* 3.2 35.2 + - - +
87I LEU* 2.9 30.4 + - + +
121I PHE* 3.8 28.3 - - + -
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Residues in contact with SER 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I PHE* 3.4 27.3 - - - -
57I VAL* 5.5 0.5 - - - +
58I GLN* 3.0 39.0 + - - -
61I MET* 3.8 1.2 - - - +
80I LEU 3.0 15.5 + - - -
81I GLN 3.7 2.0 - - - -
82I GLU 3.1 0.4 - - - -
83I LEU* 1.3 75.4 - - - +
85I LEU* 1.3 62.7 + - - +
87I LEU* 4.0 1.1 - - - -
88I LYS* 3.1 28.2 + - - +
121I PHE* 3.7 14.0 - - - -
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Residues in contact with LEU 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 5.8 0.7 - - - +
78D VAL* 4.4 20.9 - - + +
81D GLN* 3.6 40.2 - - + +
82D GLU* 3.6 43.3 - - + +
85D LEU* 3.7 21.1 - - + -
58I GLN* 4.5 11.0 - - - +
81I GLN 3.4 10.0 + - - +
82I GLU* 3.0 9.3 + - - +
84I SER* 1.3 78.8 - - - +
86I ARG* 1.3 61.9 + - - +
87I LEU 3.5 0.2 + - - -
88I LYS* 3.6 21.8 + - + +
89I SER* 4.7 2.9 + - - -
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Residues in contact with ARG 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D VAL* 5.5 2.2 - - - -
82D GLU* 3.9 18.2 - - - +
30F SER* 4.2 28.1 + - - -
32F GLN* 3.7 34.1 - - - +
107F TYR* 5.3 1.6 - - + -
10I MET* 2.9 45.7 + - + +
15I HIS* 4.1 18.8 + - - -
79I GLN* 4.7 2.4 + - - +
82I GLU* 3.1 24.0 + - - +
83I LEU* 3.4 50.4 - - - +
85I LEU* 1.3 77.2 - - - +
87I LEU* 1.3 60.4 + - - +
88I LYS 3.5 0.5 + - - -
89I SER* 3.6 12.9 + - - -
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I MET* 3.8 28.3 - - + -
11I ILE* 3.8 25.4 - - + -
54I PHE* 3.4 35.0 - - + -
83I LEU* 2.9 32.1 + - + +
84I SER* 3.2 0.8 + - - -
86I ARG* 1.3 74.2 - - - +
88I LYS* 1.3 51.9 + - - +
89I SER 2.9 5.8 - - - -
90I CYS* 2.7 35.7 + - + +
91I PHE* 3.4 13.8 - - + -
121I PHE* 4.5 5.6 - - + -
124I THR* 5.0 2.5 - - + -
128I LEU* 4.0 23.6 - - + -
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Residues in contact with LYS 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 2.6 35.9 + - - +
69D ASP* 5.0 7.1 - - - +
78D VAL* 6.5 0.7 - - + -
81D GLN* 5.9 2.5 - - - +
54I PHE* 4.1 13.0 - - + -
55I LEU* 4.6 12.8 - - + +
58I GLN* 4.0 30.0 - - - +
84I SER 3.1 14.2 + - - +
85I LEU* 3.8 18.6 - - + +
86I ARG 3.3 1.2 - - - -
87I LEU* 1.3 75.0 - - - +
89I SER* 1.3 56.0 + - - +
90I CYS 3.1 1.6 - - - -
91I PHE* 3.2 25.3 - - - +
93I LYS* 3.9 31.3 - - - +
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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