Contacts of the helix formed by residues 12 - 25 (chain G) 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 GLY 12 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G HIS 5.3 2.5 - - - -
10G MET 3.2 8.6 + - - -
11G ILE* 1.3 75.9 - - - +
13G SER* 1.3 66.7 + - - -
14G GLY 3.1 3.6 - - - -
15G HIS* 3.2 28.6 + - - +
16G LEU* 3.7 8.8 + - - +
125G LYS* 4.5 4.0 - - - -
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Residues in contact with SER 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G GLY* 1.3 68.8 - - - -
14G GLY* 1.3 59.9 + - - +
16G LEU* 3.1 14.8 + - - +
17G GLN* 2.9 46.8 + - - +
125G LYS* 4.6 11.7 + - - +
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Residues in contact with GLY 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G GLY* 3.1 1.8 - - - -
13G SER* 1.3 79.8 - - - +
15G HIS* 1.3 58.9 + - - +
17G GLN* 3.8 13.1 - - - +
18G SER* 3.2 26.0 + - - -
79G GLN* 5.8 0.2 - - - +
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Residues in contact with HIS 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G MET 3.9 17.7 + - - -
11G ILE* 4.3 5.5 - - + -
12G GLY* 3.2 27.8 + - - +
13G SER 3.1 0.8 - - - -
14G GLY* 1.3 78.2 + - - +
16G LEU* 1.3 60.2 + - + +
18G SER* 2.8 19.9 + - - -
19G LEU* 3.1 22.5 + - + +
79G GLN* 4.4 21.5 + - + +
80G LEU* 4.2 14.9 - - + +
83G LEU* 3.9 35.6 - - + +
86G ARG* 4.4 10.7 + - - -
121G PHE* 6.2 0.2 - - + -
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Residues in contact with LEU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 4.3 15.0 - - + -
12G GLY 3.9 10.5 - - - +
13G SER* 3.1 12.0 + - - +
15G HIS* 1.3 75.1 - - - +
17G GLN* 1.3 60.7 + - + +
19G LEU* 3.3 19.4 + - + +
20G GLN* 2.9 25.3 + - - +
118G LYS* 3.5 27.2 - - - +
121G PHE* 4.4 1.6 - - + -
122G ASN* 4.0 35.7 - - + +
125G LYS* 3.9 25.6 - - + +
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Residues in contact with GLN 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G SER* 2.9 35.6 + - - +
14G GLY* 3.8 9.7 - - - +
16G LEU* 1.3 77.2 - - + +
18G SER* 1.3 56.1 + - - +
20G GLN* 3.2 6.1 + - - +
21G ARG* 3.0 61.8 + - + +
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Residues in contact with SER 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G GLY 3.2 13.4 + - - -
15G HIS* 2.8 24.8 + - - -
17G GLN* 1.3 78.8 - - - +
19G LEU* 1.3 59.7 + - - +
21G ARG* 3.9 11.2 + - - +
22G LEU* 3.2 27.4 + - - +
73G ASN* 5.3 0.9 - - - +
76G ALA* 4.3 22.7 + - - +
79G GLN* 5.1 8.8 + - - +
80G LEU* 4.6 9.2 - - - +
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS* 3.1 21.6 + - + +
16G LEU* 3.4 19.5 - - + +
17G GLN 3.1 0.2 - - - -
18G SER* 1.3 76.8 + - - +
20G GLN* 1.3 60.5 + - - +
22G LEU* 3.2 13.5 + - + +
23G ILE* 3.0 32.1 + - + +
80G LEU* 3.5 28.9 - - + -
114G LEU* 5.1 7.0 - - + +
117G VAL* 4.1 22.0 - - + -
118G LYS* 3.5 24.7 - - + +
121G PHE* 3.9 31.9 - - + -
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Residues in contact with GLN 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU 2.9 16.1 + - - +
17G GLN* 3.2 7.2 + - - +
19G LEU* 1.3 74.0 - - - +
21G ARG* 1.3 61.2 + - + +
23G ILE* 2.9 22.7 + - - +
24G ASP* 2.8 64.3 + - - +
115G GLU* 5.4 5.1 + - - +
118G LYS* 3.8 18.7 - - - +
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Residues in contact with ARG 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G GLN* 3.0 48.7 + - - +
18G SER* 4.1 8.1 - - - +
20G GLN* 1.3 76.4 - - + +
22G LEU* 1.3 61.8 + - - +
24G ASP* 3.9 10.6 - - - +
25G SER* 3.1 26.5 + - - -
73G ASN* 4.6 5.0 - - - +
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Residues in contact with LEU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G SER 3.2 15.2 + - - +
19G LEU* 3.2 11.4 + - + +
20G GLN 3.0 0.2 - - - -
21G ARG* 1.3 78.6 - - - +
23G ILE* 1.3 58.6 + - - +
25G SER* 2.9 18.5 + - - -
26G GLN* 3.2 18.2 + - - +
67G PHE* 3.8 18.4 - - + -
73G ASN* 3.8 23.3 + - + +
76G ALA* 3.7 26.7 - - + -
77G ILE* 3.7 25.8 - - + -
80G LEU* 5.0 6.5 - - + -
114G LEU* 3.1 37.7 - - + -
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Residues in contact with ILE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 3.0 19.1 + - + +
20G GLN* 2.9 23.9 + - - +
22G LEU* 1.3 76.7 - - - +
24G ASP* 1.3 66.7 + - - +
26G GLN* 3.3 18.5 + - - +
111G LEU* 3.5 37.3 - - + +
114G LEU* 3.5 44.4 - - + +
115G GLU* 3.8 18.4 - - - +
118G LYS* 3.9 25.1 - - + -
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Residues in contact with ASP 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G GLN* 2.8 54.0 + - - +
21G ARG* 3.9 9.2 + - - +
23G ILE* 1.3 75.3 - - - +
25G SER* 1.3 60.8 + - - +
26G GLN 3.1 8.1 + - - +
111G LEU* 5.8 0.6 - - - +
67H PHE* 4.4 4.3 - - - -
68H ARG* 4.6 15.1 + - - +
71H THR* 3.7 42.4 + - + +
72H PRO* 5.5 3.8 - - + -
73H ASN* 5.2 0.2 - - - +
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Residues in contact with SER 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG 3.1 13.2 + - - -
22G LEU 2.9 18.4 + - - -
24G ASP* 1.3 76.4 - - - +
26G GLN* 1.3 62.1 + - - +
73G ASN* 3.0 18.7 + - - -
25H SER* 3.8 15.5 - - - -
26H GLN* 2.8 15.3 + - - -
67H PHE* 3.6 1.3 - - - -
71H THR* 5.8 0.7 - - - -
72H PRO* 6.3 1.6 - - - -
73H ASN* 2.8 35.2 + - - +
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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