Contacts of the helix formed by residues 45 - 64 (chain C) 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 ASP 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C LEU* 3.7 3.8 - - + +
44C LYS* 1.3 74.8 - - - +
46C PRO* 1.3 68.8 - - - +
47C VAL 3.5 3.3 + - - -
48C CYS* 2.9 45.2 + - + -
49C TYR* 2.8 31.2 + - - +
137C LYS* 3.5 23.2 + - - -
142C SER* 4.0 19.4 + - - +
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Residues in contact with PRO 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LYS 3.0 9.4 - - - +
45C ASP* 1.3 90.3 - - - +
47C VAL* 1.3 67.7 + - + +
49C TYR* 3.2 8.3 + - + +
50C LEU* 3.2 27.6 + - + +
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASP* 3.5 7.7 + - - +
46C PRO* 1.3 82.4 - - + +
48C CYS* 1.3 65.4 + - - +
50C LEU* 3.0 19.3 + - - +
51C LYS* 3.0 16.1 + - + +
127C LEU* 5.8 1.1 - - + -
134C ILE* 3.5 49.6 - - + +
135C PHE* 4.2 11.0 - - + -
137C LYS* 3.5 36.1 - - + +
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Residues in contact with CYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.4 12.4 - - + +
45C ASP* 2.9 33.3 + - + +
47C VAL* 1.3 74.5 - - - +
49C TYR* 1.3 61.3 + - - +
51C LYS* 3.7 2.0 - - - +
52C LYS 3.3 17.3 + - - -
137C LYS* 4.0 10.8 - - - -
138C ASN 4.8 0.2 - - - -
139C CYS* 2.0 54.7 - - + -
142C SER* 3.4 24.0 - - - -
143C PHE* 3.5 11.3 - - + -
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Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.5 23.2 - + - -
38C VAL* 3.6 34.0 + - + +
40C GLN* 3.7 43.8 + - + +
43C LEU* 3.6 27.8 - - + +
44C LYS 5.1 0.7 - - - +
45C ASP 2.8 20.6 + - - +
46C PRO* 3.3 9.4 - - + +
47C VAL 3.1 0.2 - - - -
48C CYS* 1.3 79.0 - - - +
50C LEU* 1.3 73.0 + - + +
52C LYS* 3.6 0.5 + - - -
53C ALA* 3.0 40.5 + - + +
116C LYS* 5.8 0.7 - - - -
119C ASN* 6.0 2.2 - - - -
120C VAL* 5.5 2.7 - - + -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PRO 3.2 13.4 + - - +
47C VAL* 3.0 9.2 + - - +
49C TYR* 1.3 91.9 - - + +
51C LYS* 1.3 60.1 + - - +
53C ALA* 3.6 2.5 - - - +
54C PHE* 2.8 33.1 + - - +
91C PHE* 4.7 0.4 - - - -
119C ASN* 5.3 2.0 - - - +
120C VAL* 4.7 18.0 - - + +
123C GLU* 4.3 26.2 - - + +
124C THR* 4.6 12.3 + - - +
127C LEU* 3.5 32.5 - - + -
135C PHE* 3.8 22.4 - - + -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 3.0 23.7 + - + +
48C CYS* 3.7 7.4 - - - +
50C LEU* 1.3 79.0 - - - +
52C LYS* 1.3 61.5 + - - +
54C PHE* 3.2 9.9 + - - +
55C LEU* 3.3 19.2 + - - +
91C PHE* 3.9 22.7 - - + -
92C THR* 2.9 23.7 + - - -
94C ASP* 2.9 23.5 + - - +
97C GLU* 5.3 2.2 - - - -
135C PHE* 3.5 35.6 + - + +
137C LYS 2.9 22.3 + - - +
139C CYS* 3.5 21.3 - - - -
143C PHE* 4.6 6.3 - - + -
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Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 4.1 5.4 - - + -
43C LEU* 4.2 4.5 - - + -
48C CYS 3.3 14.0 + - - +
49C TYR 4.2 1.6 - - - +
51C LYS* 1.3 78.4 - - - +
53C ALA* 1.3 63.1 + - - +
55C LEU* 3.3 15.8 + - + +
56C LEU* 3.1 46.6 + - + +
96C GLU 4.9 1.6 + - - -
97C GLU* 4.5 5.5 - - - +
98C HIS* 3.8 23.8 - - - +
99C ASP* 3.9 16.4 + - - +
101C ALA* 3.2 25.1 - - - +
102C CYS* 3.9 13.2 - - + -
103C VAL* 4.3 4.4 - - + +
143C PHE* 3.9 37.1 - - + -
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 4.1 8.5 - - + -
38C VAL* 3.4 19.2 - - + +
49C TYR* 3.0 27.4 + - + +
50C LEU* 3.6 9.2 - - - +
52C LYS* 1.3 78.9 - - - +
54C PHE* 1.3 57.2 + - - +
56C LEU* 3.4 3.2 + - - +
57C VAL* 2.9 34.8 + - - +
120C VAL* 4.0 21.3 - - + -
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Residues in contact with PHE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU 2.8 17.3 + - - +
51C LYS 3.6 4.9 - - - +
52C LYS 3.2 0.2 - - - -
53C ALA* 1.3 75.4 - - - +
55C LEU* 1.3 68.9 + - + +
56C LEU 3.4 0.2 + - - -
57C VAL* 3.4 6.5 + - + +
58C GLN* 3.0 52.9 + - + +
84C SER* 4.0 20.4 - - - -
87C LEU* 3.6 35.4 - - + -
88C LYS* 3.9 14.1 - - + -
91C PHE* 3.8 35.4 - + + -
120C VAL* 4.4 16.5 - - + +
121C PHE* 4.3 17.0 - + - -
124C THR* 5.0 6.5 - - + +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LYS* 3.3 13.9 + - + +
52C LYS* 3.3 19.5 + - + +
54C PHE* 1.3 85.1 - - + +
56C LEU* 1.3 63.4 + - + +
58C GLN* 3.5 30.0 + - - +
59C ASP* 3.6 13.8 + - - +
88C LYS* 5.3 8.1 - - + -
91C PHE* 6.1 6.1 - - + -
97C GLU* 3.7 46.9 - - + +
98C HIS* 4.0 33.5 - - + +
143C PHE* 6.3 1.3 - - + -
62H GLU* 4.9 1.1 - - - +
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 4.1 22.4 - - + +
37C PHE* 4.0 6.5 - - + -
38C VAL* 3.3 37.9 - - + +
52C LYS* 3.1 31.1 + - + +
53C ALA* 3.8 3.8 - - - +
55C LEU* 1.3 76.3 - - + +
57C VAL* 1.3 64.9 + - - +
58C GLN 3.1 2.0 - - - -
59C ASP* 3.1 18.1 + - + +
60C ILE* 2.9 26.5 + - - +
98C HIS* 5.9 5.4 - - - +
99C ASP 5.7 1.8 - - - +
100C LYS* 5.3 5.6 - - - +
103C VAL* 3.9 25.4 - - + -
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PHE* 3.9 17.9 - - + -
53C ALA 2.9 25.0 + - - +
54C PHE* 3.8 9.4 - - + +
55C LEU 3.4 0.4 - - - -
56C LEU* 1.3 76.7 - - - +
58C GLN* 1.3 58.5 + - + +
60C ILE* 3.3 9.6 + - - +
61C MET* 2.9 33.8 + - + +
117C VAL* 4.0 22.2 - - + -
120C VAL* 4.1 23.1 - - + -
121C PHE* 3.5 35.4 - - + -
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Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 3.0 47.0 + - + +
55C LEU* 3.6 18.8 - - - +
56C LEU 3.1 0.2 - - - -
57C VAL* 1.3 76.4 - - + +
59C ASP* 1.3 64.3 + - - +
61C MET* 3.5 10.7 + - + +
62C GLU* 3.2 25.1 + - - +
81C GLN* 4.7 2.1 + - - -
84C SER* 3.9 20.8 + - - +
88C LYS* 3.3 24.3 - - - +
62H GLU* 2.5 39.2 - - - +
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Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU 3.6 11.8 + - - +
56C LEU* 3.1 20.3 + - + +
58C GLN* 1.3 77.3 - - - +
60C ILE* 1.3 58.7 + - + +
62C GLU* 4.7 2.5 - - - -
63C ASP* 2.9 46.4 + - - +
98C HIS* 3.9 6.4 + - - -
59H ASP* 4.5 5.6 - - - +
62H GLU* 3.8 10.7 - - - +
63H ASP* 2.7 37.8 - - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 4.3 11.4 - - + -
36C GLU* 3.6 24.7 - - + +
37C PHE* 3.7 23.3 - - + -
56C LEU 2.9 19.5 + - - +
57C VAL* 3.5 12.1 - - + +
58C GLN 3.2 0.2 - - - -
59C ASP* 1.3 76.5 - - + +
61C MET* 1.3 59.6 + - - +
64C THR* 2.8 33.1 + - - +
65C MET* 2.9 33.4 + - + -
113C LEU* 3.9 34.1 - - + -
117C VAL* 4.4 3.6 - - + -
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Residues in contact with MET 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C VAL* 2.9 24.6 + - + +
58C GLN* 4.0 12.3 - - + +
59C ASP 3.4 0.2 - - - -
60C ILE* 1.3 76.9 - - - +
62C GLU* 1.3 60.7 + - - +
65C MET* 3.2 48.9 - - + +
77C ILE* 3.9 20.2 - - + +
80C LEU* 3.9 28.9 - - - +
81C GLN* 3.8 25.2 + - + +
84C SER* 3.7 24.7 - - - +
117C VAL* 4.9 2.2 - - + -
121C PHE* 4.0 20.0 - - + -
88H LYS* 5.7 1.0 + - - -
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN 3.2 17.6 + - - +
59C ASP* 4.0 3.6 - - - +
61C MET* 1.3 79.7 - - - +
63C ASP* 1.3 71.5 + - - +
66C ARG* 4.5 9.6 - - - +
81C GLN* 2.8 25.9 + - - +
55H LEU* 4.5 10.0 - - - +
58H GLN* 3.4 33.8 - - + +
59H ASP* 3.9 12.1 - - - +
85H LEU* 4.5 2.9 - - - +
88H LYS* 3.9 24.9 + - - +
93H LYS* 4.9 5.7 + - - -
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Residues in contact with ASP 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ASP* 2.9 26.8 + - - +
62C GLU* 1.3 86.0 - - - +
64C THR* 1.3 64.3 + - - +
66C ARG* 3.1 28.5 + - - +
55H LEU 5.2 0.3 - - - +
59H ASP* 2.9 40.0 - - - +
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Residues in contact with THR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 4.0 10.1 - - + -
34C THR 4.5 13.6 + - - +
35C PHE* 4.6 6.3 - - + +
60C ILE* 2.8 29.6 + - - +
63C ASP* 1.3 79.7 - - - +
65C MET* 1.3 59.1 + - - +
66C ARG* 3.0 17.5 + - - +
113C LEU* 3.8 24.7 - - + -
27D MET* 3.7 16.8 - - + +
28D GLU 4.3 7.4 - - - +
29D THR* 5.4 0.6 - - + +
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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