Contacts of the helix formed by residues 15 - 27 (chain C) in PDB entry 3UNF
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 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C THR* 4.0 5.6 - - + -
8C VAL 3.8 21.8 - - - +
9C PHE* 3.7 31.9 - - + -
14C HIS* 1.3 70.0 - - - +
16C PHE* 1.3 59.8 + - - +
17C GLN 3.3 2.2 - - - -
18C VAL* 3.2 27.4 + - + +
19C GLU* 2.9 34.4 + - - +
118C THR* 5.1 0.9 - - - -
149C SER* 6.6 0.2 - - - -
73D LEU* 3.7 25.1 - - + -
76D ASP* 5.3 0.2 - - - +
127D ARG* 3.5 35.2 - - - +
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Residues in contact with PHE 16 (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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8C VAL 4.3 4.9 + - - +
10C SER* 3.2 30.5 + - - +
11C PRO* 5.8 0.4 - - + -
12C ASP* 4.4 11.4 - - - -
14C HIS* 3.4 14.0 + + + -
15C LEU* 1.3 72.0 - - - +
17C GLN* 1.3 53.7 + - + +
19C GLU* 3.1 22.8 + - - +
20C TYR* 2.7 74.0 + + + -
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Residues in contact with GLN 17 (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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10B ILE* 3.5 22.5 - - - +
11B PHE* 3.1 56.4 + - - +
6C ILE* 3.4 31.0 - - + +
7C THR* 3.4 25.3 - - + +
8C VAL 5.3 1.0 + - - +
15C LEU 3.3 0.6 - - - -
16C PHE* 1.3 79.1 - - + +
18C VAL* 1.3 61.2 + - - +
20C TYR* 3.6 20.4 + - - +
21C ALA* 3.2 21.1 + - - +
124C ARG* 4.3 2.8 - - - +
125C PRO* 4.1 8.3 - - + +
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Residues in contact with VAL 18 (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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7C THR* 3.7 12.8 - - + -
15C LEU* 3.2 34.7 + - + +
17C GLN* 1.3 75.2 - - - +
19C GLU* 1.3 63.3 + - + +
21C ALA* 3.3 7.2 + - - +
22C GLN* 3.2 27.8 + - - +
118C THR* 3.6 24.0 - - + -
125C PRO* 4.3 5.8 - - + -
148C PRO* 3.9 4.4 - - - +
149C SER* 3.5 41.7 - - - +
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Residues in contact with GLU 19 (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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14C HIS* 2.7 41.7 + - - +
15C LEU 2.9 19.1 + - - +
16C PHE* 3.1 26.3 + - + +
18C VAL* 1.3 74.8 - - + +
20C TYR* 1.3 67.4 + - + +
22C GLN* 3.2 22.4 + - - +
23C GLU* 3.2 24.5 + - - +
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Residues in contact with TYR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.6 39.0 - - + -
12B SER 3.6 9.9 - - - +
13B PRO* 3.6 41.6 - - + +
15B GLY* 3.3 14.3 - - - -
16C PHE* 2.7 60.4 + + + +
17C GLN* 3.6 22.4 - - - +
18C VAL 3.3 0.2 - - - -
19C GLU* 1.3 75.3 - - + +
21C ALA* 1.3 59.7 + - - +
23C GLU* 3.1 18.9 + - + +
24C ALA* 3.2 8.8 + - - +
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Residues in contact with ALA 21 (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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11B PHE* 4.2 21.7 - - + -
17C GLN 3.2 12.4 + - - +
18C VAL 3.4 9.9 - - - +
19C GLU 3.2 0.2 - - - -
20C TYR* 1.3 78.8 - - - +
22C GLN* 1.3 57.9 + - - +
24C ALA* 3.4 5.5 + - - +
25C VAL* 3.3 18.9 + - - +
125C PRO* 4.3 4.9 - - + -
126C PHE 3.4 24.2 - - - +
127C GLY* 4.1 3.8 - - - -
148C PRO* 3.6 18.2 - - + +
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Residues in contact with GLN 22 (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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18C VAL* 3.2 15.2 + - - +
19C GLU* 3.3 37.5 + - - +
20C TYR 3.2 0.2 - - - -
21C ALA* 1.3 73.6 - - - +
23C GLU* 1.3 63.4 + - - +
24C ALA 3.3 0.2 - - - -
25C VAL* 3.0 26.9 - - + +
26C LYS* 3.3 22.4 + - - +
147C ASP* 4.3 15.9 - - + +
148C PRO* 4.1 17.3 - - + -
149C SER* 4.5 9.0 - - - -
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Residues in contact with GLU 23 (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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13B PRO 3.9 16.2 - - - +
14B GLU* 3.5 20.7 - - - +
19C GLU 3.2 13.5 + - - +
20C TYR* 3.1 13.8 + - + +
22C GLN* 1.3 77.7 - - - +
24C ALA* 1.3 62.4 + - - +
26C LYS* 3.4 23.3 + - - +
27C LYS* 3.2 27.2 + - - +
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Residues in contact with ALA 24 (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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11B PHE* 4.3 6.7 - - + -
15B GLY* 3.4 23.5 - - - +
20C TYR 3.2 8.4 + - - +
21C ALA* 3.4 12.1 - - - +
22C GLN 3.3 0.2 - - - -
23C GLU* 1.3 76.9 - - - +
25C VAL* 1.3 61.0 + - - +
27C LYS* 3.4 10.5 + - - +
28C GLY 3.3 13.7 + - - -
74C GLY* 3.4 12.0 - - - -
75C LEU* 4.2 17.7 - - + +
127C GLY* 4.0 11.7 - - - +
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Residues in contact with VAL 25 (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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21C ALA 3.3 6.0 + - - +
22C GLN* 3.0 36.1 - - + +
24C ALA* 1.3 78.7 - - - +
26C LYS* 1.3 62.5 + - + +
28C GLY* 2.9 15.2 + - - -
73C ALA* 3.1 30.2 - - + +
74C GLY* 3.8 6.7 - - - -
127C GLY 4.2 2.4 + - - +
128C ILE 4.6 0.9 - - - -
129C SER* 3.4 37.0 - - - +
148C PRO* 4.9 0.7 - - + -
160C ILE* 4.7 2.2 - - + -
161C GLY* 3.2 24.5 - - - +
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Residues in contact with LYS 26 (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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22C GLN* 3.3 22.9 + - - +
23C GLU* 3.8 26.0 + - - +
24C ALA 3.3 0.4 - - - -
25C VAL* 1.3 82.2 - - + +
27C LYS* 1.3 56.4 + - - +
28C GLY 3.2 0.9 - - - -
161C GLY* 4.1 11.4 - - - +
162C ARG* 2.8 57.1 + - - +
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Residues in contact with LYS 27 (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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14B GLU* 4.5 29.7 + - - +
15B GLY 5.8 2.5 - - - +
16B ARG* 5.7 9.4 - - + +
23C GLU 3.2 15.8 + - - +
24C ALA* 3.6 11.7 - - - +
25C VAL 3.2 0.2 - - - -
26C LYS* 1.3 75.0 - - - +
28C GLY* 1.3 64.2 + - - +
46C LYS* 4.8 6.1 + - - -
162C ARG* 4.4 10.3 - - - +
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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
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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