Contacts of the helix formed by residues 25 - 37 (chain A) in PDB entry 1TW2
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLY 3.4 4.8 + - - -
24A SER* 1.3 71.5 - - - +
26A HIS* 1.3 69.4 + - - +
27A THR 3.4 0.4 - - - -
28A PRO* 3.4 3.8 - - - +
29A MET* 3.4 29.5 + - + +
120A THR* 5.9 1.3 - - + -
25B LEU* 3.8 26.7 - - + -
28B PRO* 3.9 20.0 - - + -
29B MET* 4.0 26.7 - - - -
32B ARG* 3.8 18.6 - - - +
116B ASP* 3.4 41.7 - - + +
117B ILE* 4.2 11.0 - - + +
119B PHE* 4.7 5.6 - - + -
120B THR* 5.1 8.1 - - + -
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Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 3.5 10.1 + - - +
25A LEU* 1.3 78.7 + - - +
27A THR* 1.3 53.1 + - - +
29A MET* 3.1 5.0 + - - +
30A VAL* 2.8 40.9 + - + +
70A HIS* 4.1 13.0 - - + +
32B ARG* 5.8 0.6 + - - -
116B ASP* 4.4 0.8 + - - -
119B PHE* 3.1 50.7 - + - -
297B THR 3.9 7.9 - - - -
298B GLU* 2.8 53.4 + - + +
301B LEU* 4.1 6.5 - - + -
302B ARG* 3.4 29.3 + - + -
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG 5.8 0.9 - - - -
24A SER* 3.3 17.1 + - - -
26A HIS* 1.3 77.1 - - - +
28A PRO* 1.3 66.2 - - + +
30A VAL* 3.0 4.7 + - - +
31A VAL* 2.9 30.0 + - - +
70A HIS* 3.1 25.3 + - - -
74A ILE* 3.8 20.2 - - + +
22B LEU* 3.6 38.8 - - + +
294B GLU* 5.5 1.4 + - - +
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Residues in contact with PRO 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER 3.2 21.5 - - - +
25A LEU 3.4 12.1 - - - +
27A THR* 1.3 94.1 - - + +
29A MET* 1.3 54.4 + - - +
31A VAL* 3.2 1.3 + - + +
32A ARG* 2.9 37.6 + - - +
22B LEU 3.3 12.7 - - - +
23B GLY* 3.4 18.8 - - - +
24B SER 3.4 27.1 - - - +
25B LEU* 3.8 17.0 - - + -
28B PRO* 4.2 2.2 - - + -
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Residues in contact with MET 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.4 21.7 + - + +
26A HIS 3.1 4.3 + - - +
28A PRO* 1.3 77.0 - - - +
30A VAL* 1.3 53.8 + - - +
32A ARG* 3.5 11.8 + - - +
33A THR* 2.7 43.8 + - + +
108A LEU* 3.9 29.8 - - + -
117A ILE* 6.3 2.2 - - + -
25B LEU* 3.8 26.9 - - + -
119B PHE* 3.3 44.4 - - + +
120B THR* 3.7 24.5 - - - +
122B LEU* 4.7 5.4 - - + +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A HIS* 2.8 22.1 + - - +
27A THR 3.4 7.0 - - - +
29A MET* 1.3 70.8 - - - +
31A VAL* 1.3 66.4 + - - +
33A THR* 4.1 1.4 + - - -
34A ALA* 3.0 23.6 + - - +
67A LEU* 4.0 30.0 - - + +
70A HIS* 3.3 31.2 - - + +
71A LEU* 3.5 31.0 - - + +
74A ILE* 4.7 2.2 - - + -
119B PHE* 6.0 1.3 - - + -
122B LEU* 5.1 5.8 - - + -
301B LEU* 4.2 14.6 - - + -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR 2.9 17.1 + - - +
28A PRO 3.6 6.1 - - - +
30A VAL* 1.3 76.9 - - - +
32A ARG* 1.3 57.7 + - - +
34A ALA* 3.2 6.8 + - - +
35A ALA* 3.0 25.1 + - - +
71A LEU* 4.8 0.2 - - - -
74A ILE* 4.0 11.7 - - + -
76A LEU* 3.8 24.9 - - + -
94A LEU* 4.5 7.5 - - + +
106A HIS* 4.1 14.8 - - + +
19B LEU* 4.0 20.4 - - + -
22B LEU* 3.9 22.2 - - + +
23B GLY* 4.0 16.6 - - - -
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 2.9 20.3 + - - +
29A MET* 3.9 22.4 - - - +
31A VAL* 1.3 77.2 - - - +
33A THR* 1.3 57.6 + - - +
35A ALA* 3.3 0.4 + - - -
36A THR* 2.7 31.8 + - - -
105A TRP 4.4 5.9 + - - -
106A HIS* 3.2 37.2 + - + +
108A LEU* 4.1 18.2 - - + -
113A ALA* 3.3 25.3 + - - +
116A ASP* 3.2 38.2 + - - +
302A ARG* 3.8 9.7 - - - +
23B GLY 2.9 26.6 + - - +
24B SER* 4.2 1.4 - - - +
25B LEU* 3.7 21.6 - - - +
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A MET* 2.7 27.2 + - + +
30A VAL* 4.3 1.3 - - - -
32A ARG* 1.3 73.0 - - - +
34A ALA* 1.3 67.9 + - - +
35A ALA 3.1 0.2 - - - -
36A THR* 3.8 5.6 - - - -
37A LEU* 3.1 34.2 + - - +
67A LEU* 3.5 23.4 - - - +
108A LEU* 4.7 2.2 - - + -
122B LEU* 3.4 35.2 - - + +
123B PRO* 3.7 27.4 - - + -
126B ILE* 4.6 1.0 - - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL 3.0 18.3 + - - +
31A VAL* 3.5 4.9 - - - +
33A THR* 1.3 80.9 + - - +
35A ALA* 1.3 58.5 + - - +
37A LEU* 3.6 1.0 + - - -
38A ARG 3.5 1.2 + - - -
39A LEU* 3.1 44.8 + - + +
40A VAL* 4.7 2.1 + - + -
67A LEU* 4.5 2.9 - - + +
71A LEU* 3.8 31.6 - - + -
94A LEU* 4.7 11.9 - - + -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL 3.0 13.4 + - - +
32A ARG 3.7 8.1 - - - +
33A THR 3.1 0.2 - - - -
34A ALA* 1.3 74.4 - - - +
36A THR* 1.3 63.5 + - - +
38A ARG* 3.1 6.5 + - - +
94A LEU* 4.0 18.8 - - + +
103A ARG* 3.0 54.5 + - + +
106A HIS* 4.0 15.9 - - + +
107A ASP* 4.9 0.4 - - - -
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG 2.7 21.5 + - - -
33A THR* 3.8 8.5 - - - -
35A ALA* 1.3 75.5 - - - +
37A LEU* 1.3 61.9 + - - +
38A ARG* 3.2 6.3 + - - +
103A ARG* 4.4 3.5 + - - -
107A ASP* 3.6 26.6 - - - +
108A LEU* 3.1 34.5 + - + +
109A THR* 4.8 9.0 - - - +
123B PRO* 5.1 4.5 - - + -
127B ARG* 4.2 20.3 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 3.1 34.7 + - - +
34A ALA 4.0 0.9 - - - +
35A ALA 3.2 0.2 - - - -
36A THR* 1.3 77.4 - - - +
38A ARG* 1.3 70.0 + - - +
39A LEU* 3.3 27.1 + - + -
42A HIS* 3.4 14.4 + - - -
57A THR* 3.6 25.8 - - + +
59A THR* 4.1 20.2 - - + -
64A LEU* 4.7 0.4 - - + -
67A LEU* 4.4 4.0 - - + -
123B PRO* 5.3 3.8 - - + +
126B ILE* 4.3 13.2 - - + -
127B ARG* 4.0 33.7 - - + +
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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