Contacts of the helix formed by residues 25 - 35 (chain G) in PDB entry 4QLC
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 PRO 25 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17G SER* 3.9 9.0 - - - +
23G GLN 4.0 0.6 - - - -
24G PHE* 1.3 86.9 - - + +
26G VAL* 1.3 66.0 + - - +
27G GLY* 3.1 1.6 - - - +
28G ARG* 3.7 27.8 - - + +
29G ILE* 3.1 37.4 + - + +
51G ALA* 4.9 0.9 - - - -
34H TYR* 4.8 6.5 - - + -
37H TYR* 3.4 49.8 - - + +
132I G 4.8 3.6 - - - +
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Residues in contact with VAL 26 (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 ARG* 4.0 44.4 - - + +
17G SER* 3.8 6.8 + - - -
20G ALA* 4.6 0.4 - - + -
22G LEU* 3.9 28.3 - - + -
24G PHE 3.2 7.0 + - - +
25G PRO* 1.3 71.0 - - - +
27G GLY* 1.3 57.5 + - - +
29G ILE* 4.0 1.7 - - - -
30G HIS* 3.0 29.3 + - + +
47G PRO* 3.9 8.1 - - + +
48G VAL* 3.7 39.7 - - + +
51G ALA* 4.3 8.1 - - + -
118H TYR* 4.9 0.9 - - + -
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Residues in contact with GLY 27 (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 ARG* 5.4 0.9 - - - -
17G SER* 4.9 1.8 + - - -
25G PRO* 3.1 1.8 - - - +
26G VAL* 1.3 81.3 - - - +
28G ARG* 1.3 60.8 + - - +
30G HIS* 3.4 5.5 + - - +
31G ARG* 3.3 21.1 + - - +
40J G 4.2 16.6 + - - +
41J A 3.2 31.3 + - - -
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Residues in contact with ARG 28 (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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25G PRO* 3.3 27.9 + - + +
27G GLY* 1.3 74.6 - - - +
29G ILE* 1.3 66.3 + - + +
31G ARG* 3.2 30.6 + - - +
32G LEU* 3.0 32.5 + - + +
32H GLU* 3.1 28.1 + - - +
33H SER 2.7 22.8 + - - -
34H TYR* 4.9 7.1 - - + +
37H TYR* 3.5 18.8 + - - +
132I G 3.2 21.5 + - - -
133I C 2.3 29.3 + - - -
39J G 6.1 0.6 - - - -
40J G 3.1 26.2 + - - +
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Residues in contact with ILE 29 (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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24G PHE* 5.4 0.4 - - + -
25G PRO* 3.1 31.9 + - + +
26G VAL* 4.0 2.5 - - - +
28G ARG* 1.3 79.5 - - + +
30G HIS* 1.3 64.8 + - - +
32G LEU* 3.3 8.0 + - - +
33G LEU* 3.1 25.1 + - + +
47G PRO* 3.5 34.5 - - + +
50G LEU* 4.3 9.6 - - + -
51G ALA* 4.4 9.0 - - + -
54G MET* 4.2 16.6 - - + -
34H TYR* 3.8 32.5 - - + +
67H PHE* 4.1 21.6 - - + -
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Residues in contact with HIS 30 (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 ARG* 3.3 29.8 + - - +
26G VAL* 3.0 19.8 + - + +
27G GLY* 3.6 6.3 - - - +
28G ARG 3.3 0.2 - - - -
29G ILE* 1.3 77.4 - - - +
31G ARG* 1.3 62.7 + - - +
33G LEU* 3.5 3.9 + - - +
34G ARG* 3.1 60.7 + - - +
42G VAL* 3.9 27.9 + - + +
43G GLY 5.1 1.4 + - - -
44G ALA* 5.7 3.5 - - - -
47G PRO* 3.6 23.8 - - + +
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Residues in contact with ARG 31 (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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27G GLY 3.3 4.7 + - - +
28G ARG* 3.2 35.9 + - - +
30G HIS* 1.3 77.0 - - - +
32G LEU* 1.3 88.5 + - - +
33G LEU 3.1 2.0 - - - -
34G ARG* 2.9 27.3 + - + +
35G LYS* 3.0 47.5 + - + +
32H GLU* 4.9 9.9 - - - +
39J G 4.3 20.2 - - - -
40J G 2.9 30.9 + - - +
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Residues in contact with LEU 32 (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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28G ARG* 3.0 28.3 + - + +
29G ILE* 3.3 2.4 + - - +
31G ARG* 1.3 107.3 - - - +
33G LEU* 1.3 60.2 + - - +
35G LYS* 3.9 4.9 - - + +
36G GLY* 3.1 22.0 + - - -
38G TYR* 3.8 3.8 - - - -
32H GLU* 5.1 10.1 - - - +
34H TYR* 3.2 32.1 - - + +
64H ASN* 5.5 1.3 - - - +
67H PHE* 3.5 29.3 - - + -
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Residues in contact with LEU 33 (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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29G ILE* 3.1 20.5 + - + +
30G HIS* 3.5 7.9 - - - +
31G ARG 3.1 0.4 - - - -
32G LEU* 1.3 74.5 - - - +
34G ARG* 1.3 65.1 + - - +
36G GLY 3.3 2.4 + - - -
37G ASN 4.2 1.2 + - - -
38G TYR* 3.2 33.6 + - + +
39G ALA 5.2 1.9 + - - +
42G VAL* 3.9 33.3 - - + +
46G ALA* 4.6 6.1 - - + -
47G PRO* 4.2 24.5 - - + -
50G LEU* 4.3 8.7 - - + -
67H PHE* 4.0 13.9 - - + -
71H ALA* 4.0 27.6 - - + -
86H ILE* 5.5 10.1 - - + -
91H ILE* 4.8 4.7 - - + -
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Residues in contact with ARG 34 (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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40C GLU* 5.4 2.6 - - - +
30G HIS* 3.1 50.8 + - - +
31G ARG* 2.9 11.7 + - + +
33G LEU* 1.3 78.0 - - - +
35G LYS* 1.3 61.5 + - + +
36G GLY 3.2 2.6 + - - -
37G ASN* 4.1 6.8 + - - +
39G ALA 5.1 7.8 - - - +
42G VAL* 4.1 16.7 + - + +
123I A 2.5 56.8 + - - +
124I G 5.2 4.4 + - - -
125I T 6.3 0.8 - - - +
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Residues in contact with LYS 35 (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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40C GLU* 6.0 0.9 - - - -
79D HIS* 5.5 5.5 + - - -
31G ARG* 3.0 48.3 + - + +
32G LEU* 3.9 4.9 - - + +
34G ARG* 1.3 78.0 - - + +
36G GLY* 1.3 58.8 + - - +
37G ASN* 3.4 9.5 + - - +
39J G 5.9 3.6 + - - -
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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
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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