Contacts of the helix formed by residues 31 - 44 (chain T) in PDB entry 2P8Z
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 31 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T HIS* 1.3 70.1 - - - +
32T LYS* 1.3 62.7 + - - -
33T SER 3.2 0.9 - - - -
34T THR* 3.5 3.8 + - - -
35T LEU* 3.1 31.3 + - - +
128T VAL* 5.0 0.2 - - - -
158T ASN* 3.7 9.2 - - - -
159T LYS* 4.9 0.4 - - - -
843T GNP 1.4 60.3 + - - -
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Residues in contact with LYS 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62S THR* 6.0 7.4 - - + +
65S THR* 5.6 0.9 - - - +
66S ALA 6.0 0.7 - - - +
24T VAL* 3.3 39.7 + - + +
25T ILE* 5.1 0.6 - - - +
26T ALA* 3.6 37.9 + - + +
30T HIS 3.7 1.2 - - - -
31T GLY* 1.3 71.8 - - - +
33T SER* 1.3 63.0 + - - +
35T LEU* 3.5 3.1 + - - +
36T THR* 2.9 34.9 + - + +
104T ASP* 5.3 5.8 - - - -
105T SER* 3.0 36.8 + - - +
106T PRO 4.3 6.3 + - - -
107T GLY* 5.6 1.6 - - - -
128T VAL* 4.8 1.8 - - - -
843T GNP 2.8 19.1 + - - +
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Residues in contact with SER 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S TYR* 3.9 18.6 - - - -
50S ILE* 4.0 19.2 - - - +
51S ASP* 3.4 12.0 + - - -
62S THR* 3.2 24.6 + - - +
32T LYS* 1.3 78.0 - - - +
34T THR* 1.3 61.5 + - - +
36T THR* 3.0 10.8 + - - -
37T ASP* 2.9 31.3 + - - +
843T GNP 3.0 9.9 + - - -
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Residues in contact with THR 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S TYR* 3.1 25.8 - - + -
31T GLY 3.6 4.0 + - - -
33T SER* 1.3 74.5 - - - +
35T LEU* 1.3 63.9 + - - +
37T ASP* 3.8 11.6 - - - +
38T SER* 3.1 21.3 + - - -
214T GLY* 3.7 14.0 - - - +
215T LEU* 4.9 4.0 - - + -
843T GNP 2.4 70.3 + - + +
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Residues in contact with LEU 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T VAL* 5.6 2.7 - - + -
31T GLY 3.1 16.2 + - - +
32T LYS* 3.8 3.8 - - - +
33T SER 3.1 1.0 - - - -
34T THR* 1.3 79.6 + - - +
36T THR* 1.3 61.9 + - + +
38T SER* 3.1 8.9 + - - -
39T LEU* 3.0 29.7 + - - +
126T LEU* 5.1 6.1 - - + -
128T VAL* 3.6 39.0 - - + -
156T VAL* 4.5 16.2 - - + -
158T ASN* 4.2 10.3 - - - +
213T SER 5.1 0.2 - - - -
214T GLY* 3.5 30.5 - - - +
330T ALA* 5.5 4.7 - - + -
334T LEU* 4.2 24.0 - - + +
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Residues in contact with THR 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S ILE* 3.5 18.5 - - - +
68S VAL* 4.6 7.3 - - + +
24T VAL* 4.0 26.2 - - + -
32T LYS* 2.9 24.6 + - + +
33T SER* 3.0 10.8 + - - -
35T LEU* 1.3 74.5 - - + +
37T ASP* 1.3 63.6 + - - +
39T LEU* 3.1 9.5 + - - +
40T VAL* 2.8 35.7 + - - +
102T LEU* 3.8 18.6 - - + -
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Residues in contact with ASP 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S LYS 2.9 13.9 - - - +
46S ASP* 3.2 5.2 - - - +
47S TYR* 2.2 50.3 - - + +
50S ILE* 2.2 38.0 - - - +
33T SER 2.9 17.4 + - - +
34T THR* 3.8 6.5 - - - +
36T THR* 1.3 77.6 + - - +
38T SER* 1.3 59.5 + - - +
40T VAL* 3.2 1.7 + - - +
41T GLN* 2.8 42.5 + - + +
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Residues in contact with SER 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T THR 3.1 14.9 + - - -
35T LEU* 3.2 15.5 - - - -
37T ASP* 1.3 76.6 - - - +
39T LEU* 1.3 63.0 + - - +
41T GLN* 3.4 9.0 + - - +
42T ARG* 3.1 24.9 + - - +
214T GLY 5.0 6.7 - - - -
217T GLY* 5.1 4.7 - - - -
330T ALA* 4.0 11.6 - - - +
331T ALA* 3.7 22.9 + - - +
334T LEU* 5.2 1.9 - - - +
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Residues in contact with LEU 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S THR* 2.9 7.9 + - - +
24T VAL* 5.4 1.3 - - + -
35T LEU 3.0 15.1 + - - +
36T THR* 3.1 9.4 + - - +
38T SER* 1.3 76.0 - - - +
40T VAL* 1.3 58.1 + - - +
42T ARG* 3.3 0.3 + - - +
43T ALA* 2.8 28.1 + - - -
77T LEU* 3.8 22.2 - - + -
102T LEU* 4.0 25.6 - - + -
126T LEU* 4.9 8.3 - - + -
331T ALA* 4.2 9.9 - - + +
334T LEU* 4.0 30.1 - - + -
335T LEU* 3.8 34.3 - - + -
338T ILE* 4.4 11.9 - - + -
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Residues in contact with VAL 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S ALA* 3.5 6.2 - - - +
42S VAL* 4.4 1.6 - - + -
43S GLU 3.0 11.2 - - - +
44S VAL* 2.9 14.5 - - - +
45S LYS* 2.8 38.8 - - + +
68S VAL* 3.7 28.3 - - + -
36T THR* 2.8 24.8 + - - +
37T ASP* 3.7 3.6 - - - +
39T LEU* 1.3 74.1 - - - +
41T GLN* 1.3 57.1 + - - +
44T GLY* 2.7 30.1 + - - +
75T ILE* 3.8 13.5 - - + -
77T LEU* 4.5 4.7 - - + -
102T LEU* 5.1 0.4 - - + -
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Residues in contact with GLN 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S ALA* 3.9 7.7 + - - +
37S ALA* 3.9 9.7 + - - +
44S VAL* 3.9 22.3 - - + +
45S LYS 4.7 6.3 - - - +
46S ASP* 4.5 20.9 + - - +
37T ASP* 2.8 29.1 + - - +
38T SER* 3.9 8.0 - - - +
40T VAL* 1.3 72.9 - - - +
42T ARG* 1.3 60.8 + - - +
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Residues in contact with ARG 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S THR* 1.0 73.5 + - - +
36S ALA 2.8 2.9 + - - -
37S ALA* 3.2 19.1 + - - +
38S GLU* 3.2 35.0 + - - +
38T SER 3.1 10.0 + - - +
39T LEU 3.9 1.1 - - - +
41T GLN* 1.3 75.5 - - - +
43T ALA* 1.3 7.2 - - - +
78T TYR 5.7 0.2 + - - -
329T PRO* 5.2 4.5 - - - +
331T ALA* 3.2 34.1 - - + -
332T ASP* 2.9 31.3 + - - -
335T LEU* 4.2 12.4 - - + +
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Residues in contact with ALA 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S THR* 0.5 349.6 + - + +
36S ALA 2.6 1.2 - - - +
42S VAL* 2.7 22.5 - - - +
39T LEU 2.8 6.1 + - - -
42T ARG* 1.3 17.9 - - + +
44T GLY* 1.3 31.6 + - - +
77T LEU* 3.4 0.3 - - - -
78T TYR 2.9 21.1 + - - +
335T LEU* 4.2 8.3 - - + -
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Residues in contact with GLY 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S THR* 1.4 8.7 + - - -
36S ALA* 2.5 32.5 - - - +
39S ASN 2.8 4.0 - - - +
42S VAL* 0.8 166.3 - - - +
40T VAL* 2.7 22.8 + - - -
43T ALA* 1.3 63.7 - - - +
45T ILE* 1.3 5.5 - - - -
76T SER 3.6 4.7 - - - -
77T LEU* 4.1 2.0 - - - -
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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