Contacts of the helix formed by residues 25 - 37 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.8 25.8 - - + -
28A PRO* 3.8 16.8 - - + -
29A MET* 3.8 30.5 - - + -
32A ARG* 3.7 19.2 - - - +
116A ASP* 3.6 33.4 + - + +
117A ILE* 4.7 3.6 - - + -
119A PHE* 4.5 8.1 - - + -
120A THR* 4.6 16.6 - - + -
302A ARG* 5.8 0.2 - - - +
23B GLY 3.6 1.8 + - - -
24B SER* 1.3 72.3 - - - +
26B HIS* 1.3 67.1 + - - +
27B THR 3.2 2.0 - - - -
28B PRO* 3.2 15.7 - - - +
29B MET* 3.3 14.9 + - + +
120B THR* 5.2 3.8 - - + -
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.3 48.2 - + + -
294A GLU* 5.4 4.2 - - - +
298A GLU* 3.3 47.8 + - + +
301A LEU* 4.4 9.6 - - + -
302A ARG* 5.5 4.8 + - - +
600A ERT 5.0 6.4 - - - -
24B SER* 3.3 28.6 + - - -
25B LEU* 1.3 79.7 + - - +
27B THR* 1.3 62.3 + - - +
29B MET* 3.3 2.6 + - - +
30B VAL* 2.8 33.5 + - - +
70B HIS* 3.5 32.6 + + - -
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 22.7 - - + +
294A GLU* 6.2 0.2 - - - +
21B ARG* 5.8 1.5 - - - +
24B SER* 3.1 16.2 + - - -
25B LEU 3.2 0.2 - - - -
26B HIS* 1.3 82.1 + - - +
28B PRO* 1.3 71.7 - - + +
30B VAL* 3.1 12.6 + - - +
31B VAL* 3.1 13.5 + - - +
70B HIS* 3.1 31.2 + - + -
74B ILE* 4.0 21.8 - - + +
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Residues in contact with PRO 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 3.3 13.4 - - - +
23A GLY* 3.6 18.1 - - - +
24A SER 3.4 27.6 - - - +
25A LEU* 3.9 16.2 - - + -
28A PRO* 4.2 1.6 - - + -
24B SER 3.3 17.3 - - - +
25B LEU* 3.2 16.6 - - - +
27B THR* 1.3 94.8 - - - +
29B MET* 1.3 55.2 + - - +
31B VAL* 3.6 2.8 + - + +
32B ARG* 3.0 36.1 + - - +
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.0 27.6 - - + -
119A PHE* 3.2 43.5 - - + +
120A THR* 3.7 24.2 - - - +
122A LEU* 4.0 5.8 - - + -
123A PRO* 4.7 4.5 - - + -
25B LEU* 3.3 20.3 + - + +
26B HIS* 3.3 4.4 + - - +
27B THR 3.2 0.8 - - - -
28B PRO* 1.3 76.0 - - - +
30B VAL* 1.3 55.1 + - - +
32B ARG* 3.3 11.2 + - + +
33B THR* 2.7 40.5 + - - +
108B LEU* 3.8 33.2 - - + -
117B ILE* 5.1 2.9 - - + -
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.9 18.4 - - + -
301A LEU* 3.8 20.6 - - + -
26B HIS* 2.8 23.8 + - + +
27B THR 3.1 7.4 + - - +
29B MET* 1.3 69.1 - - - +
31B VAL* 1.3 64.6 + - - +
33B THR* 3.4 2.1 + - - -
34B ALA* 3.0 23.2 + - - +
67B LEU* 3.9 16.8 - - + +
70B HIS* 3.5 27.4 - - + +
71B LEU* 3.5 31.6 - - + +
74B ILE* 4.8 2.5 - - + -
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.2 18.2 - - + -
22A LEU* 4.0 20.2 - - + +
23A GLY* 4.1 7.0 - - - -
27B THR 3.1 12.9 + - - +
28B PRO 3.7 7.4 - - - +
30B VAL* 1.3 75.4 - - - +
32B ARG* 1.3 63.2 + - - +
34B ALA* 3.3 8.7 + - - +
35B ALA* 3.1 21.0 + - - +
71B LEU* 4.6 2.0 - - - -
74B ILE* 3.9 14.1 - - + -
76B LEU* 3.8 22.4 - - + -
94B LEU* 4.7 6.6 - - + +
106B HIS* 3.8 24.2 - - + +
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 2.7 30.1 + - - -
24A SER* 4.3 1.2 - - - +
25A LEU* 3.8 20.7 - - - +
26A HIS* 5.8 0.8 + - - -
28B PRO* 3.0 24.2 + - - +
29B MET* 3.3 18.4 + - - +
30B VAL 3.3 0.2 - - - -
31B VAL* 1.3 78.5 - - - +
33B THR* 1.3 57.3 + - - +
35B ALA 3.5 0.3 + - - -
36B THR* 2.8 32.0 + - - -
105B TRP 4.8 1.6 + - - -
106B HIS* 3.3 44.4 + - + +
108B LEU* 4.0 20.4 - - + +
113B ALA* 3.6 20.4 + - - +
116B ASP* 2.9 39.6 + - - +
302B ARG* 4.4 6.3 - - - +
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.3 22.7 - - + +
123A PRO* 3.5 37.0 - - + -
126A ILE* 4.5 3.3 - - - +
29B MET* 2.7 25.7 + - + +
30B VAL* 4.4 0.2 - - - -
32B ARG* 1.3 73.5 - - - +
34B ALA* 1.3 66.3 + - - +
36B THR* 4.2 4.9 - - - -
37B LEU* 3.0 37.1 + - - +
67B LEU* 3.4 25.5 - - - +
108B LEU* 4.4 3.8 - - + -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL 3.0 15.0 + - - +
31B VAL* 3.4 10.3 - - - +
33B THR* 1.3 79.3 + - - +
35B ALA* 1.3 58.3 + - - +
37B LEU* 4.7 0.2 - - - -
38B ARG 3.1 2.6 + - - -
39B LEU* 3.0 44.4 + - + +
40B VAL* 4.8 3.3 + - + +
67B LEU* 4.5 2.2 - - + +
71B LEU* 4.0 28.9 - - + -
94B LEU* 4.7 12.8 - - + -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL 3.1 13.6 + - - +
32B ARG 3.7 8.3 - - - +
33B THR 3.3 0.2 - - - -
34B ALA* 1.3 72.8 - - - +
36B THR* 1.3 65.6 + - - +
38B ARG* 3.0 9.8 + - - +
94B LEU* 4.2 10.5 - - + +
103B ARG* 3.3 59.8 + - + +
106B HIS* 3.7 16.8 - - + +
107B ASP* 4.4 0.6 - - - +
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 5.3 8.5 - - + -
32B ARG 2.8 21.7 + - - -
33B THR* 3.9 6.7 - - - -
35B ALA* 1.3 76.2 - - - +
37B LEU* 1.3 65.6 + - + +
38B ARG* 3.3 14.2 + - - +
107B ASP* 3.4 23.4 - - - +
108B LEU* 2.9 31.8 + - + +
109B THR* 4.2 14.8 - - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 5.6 11.4 - - + +
126A ILE* 4.3 8.5 - - + -
127A ARG* 6.1 2.0 - - + -
33B THR* 3.0 33.9 + - - +
34B ALA* 4.0 3.8 - - - +
36B THR* 1.3 77.3 - - + +
38B ARG* 1.3 72.5 + - - +
39B LEU* 3.1 5.9 + - + +
42B HIS* 3.2 14.7 + - - -
57B THR* 3.6 37.0 - - + +
59B THR* 4.0 24.2 - - + -
64B LEU* 4.5 7.6 - - + -
67B LEU* 4.2 15.3 - - + -
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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