Contacts of the helix formed by residues 12 - 23 (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 GLN 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLU* 4.6 18.4 - - + +
92A GLU* 6.0 0.9 - - - +
93A LEU* 3.9 13.7 - - + +
98A HIS* 3.0 37.9 + - + +
10B PRO* 3.5 2.0 - - - +
11B GLN* 1.3 80.7 - - + +
13B ILE* 1.3 57.3 + - - +
14B ASP 3.3 3.4 + - - -
15B ALA* 3.5 11.9 + - + +
16B LEU* 3.0 33.6 + - + +
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Residues in contact with ILE 13 (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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339A ILE 4.9 0.2 - - - +
340A PRO* 3.7 32.0 - - + +
341A TYR 5.4 0.2 - - - +
9B ARG* 4.0 19.7 - - + +
10B PRO* 3.5 35.4 - - + +
11B GLN 3.2 5.0 + - - +
12B GLN* 1.3 76.4 - - - +
14B ASP* 1.3 75.1 + - - +
16B LEU* 3.7 10.5 - - - +
17B ARG* 3.2 24.8 + - - +
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN 3.3 1.0 - - - -
13B ILE* 1.3 84.9 - - - +
15B ALA* 1.3 66.8 + - - +
17B ARG* 3.1 51.6 + - - +
18B THR* 3.1 13.6 + - - -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 4.3 25.6 - - + +
90A VAL* 4.1 21.0 - - + +
93A LEU* 3.6 19.1 - - + +
12B GLN* 3.5 14.0 + - + +
14B ASP* 1.3 77.5 - - - +
16B LEU* 1.3 58.4 + - - +
18B THR* 3.2 9.5 + - - -
19B LEU* 3.0 25.5 + - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.6 24.0 - - + -
98A HIS* 4.5 10.5 - - + -
100A ALA* 3.8 24.0 - - + -
102A GLN* 3.9 19.3 - - + -
338A THR 3.4 24.5 - - - +
339A ILE* 5.0 0.7 - - + -
340A PRO* 3.9 13.0 - - + -
10B PRO* 4.3 16.8 - - + -
12B GLN* 3.0 24.6 + - + +
13B ILE 3.8 5.6 - - - +
14B ASP 3.1 0.6 - - - -
15B ALA* 1.3 76.1 - - - +
17B ARG* 1.3 58.4 + - - +
19B LEU* 3.3 2.8 + - + +
20B ILE* 2.9 38.4 + - + +
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 5.2 3.2 - - - +
340A PRO* 4.0 21.5 - - + +
13B ILE* 3.2 15.6 + - - +
14B ASP* 3.1 43.7 + - - +
16B LEU* 1.3 73.0 - - - +
18B THR* 1.3 62.1 + - - +
19B LEU 3.4 0.2 - - - -
20B ILE* 4.0 5.2 - - - +
21B ARG* 3.1 30.0 + - - +
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Residues in contact with THR 18 (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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90A VAL* 4.5 15.3 - - + -
14B ASP 3.1 15.8 + - - -
15B ALA* 3.4 12.4 - - - -
16B LEU 3.2 0.2 - - - -
17B ARG* 1.3 76.6 - - - +
19B LEU* 1.3 59.0 + - - +
21B ARG* 3.5 6.2 + - - +
22B LEU* 3.0 46.0 + - + +
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Residues in contact with LEU 19 (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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31A VAL* 4.0 24.7 - - + -
76A LEU* 4.1 19.5 - - + -
90A VAL* 3.9 19.7 - - + +
93A LEU* 3.6 30.5 - - + -
94A LEU* 4.2 16.4 - - + -
102A GLN* 3.8 27.8 - - + -
106A HIS* 4.6 5.0 - - - +
15B ALA 3.0 16.3 + - - +
16B LEU 3.7 3.8 - - - +
18B THR* 1.3 74.7 - - - +
20B ILE* 1.3 66.0 + - - +
22B LEU* 3.1 3.8 + - + -
23B GLY* 3.0 21.3 + - - -
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Residues in contact with ILE 20 (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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102A GLN* 3.4 27.6 - - + +
106A HIS* 4.7 8.8 - - + +
294A GLU* 5.4 3.1 - - - +
298A GLU* 4.0 20.6 - - - +
339A ILE* 4.0 16.2 - - + -
340A PRO* 3.6 33.4 - - + -
600A ERT 4.3 20.6 - - + +
16B LEU* 2.9 25.0 + - + +
17B ARG* 4.3 4.5 - - - +
19B LEU* 1.3 76.4 - - - +
21B ARG* 1.3 63.1 + - - +
23B GLY* 3.5 1.6 + - - -
24B SER* 3.5 21.3 + - - -
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Residues in contact with ARG 21 (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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22A LEU* 4.1 24.2 - - - +
294A GLU* 4.0 26.9 + - - +
17B ARG 3.1 21.3 + - - +
18B THR* 3.7 6.1 - - - +
20B ILE* 1.3 76.7 - - - +
22B LEU* 1.3 63.3 + - + +
23B GLY 3.3 0.7 + - - -
24B SER* 3.3 20.4 + - - +
27B THR* 5.8 1.6 - - - +
74B ILE* 5.6 4.0 + - - +
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Residues in contact with LEU 22 (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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27A THR* 3.6 25.4 - - + +
28A PRO* 3.3 25.6 - - - +
31A VAL* 3.9 13.1 - - + +
74A ILE* 3.5 31.6 - - + +
76A LEU* 3.8 20.0 - - + -
18B THR* 3.0 37.7 + - + +
19B LEU* 3.1 4.9 + - - +
21B ARG* 1.3 78.3 - - + +
23B GLY* 1.3 56.8 + - - +
24B SER 3.5 0.7 + - - +
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 3.4 10.7 - - - +
31A VAL* 4.0 10.3 - - - +
32A ARG* 2.9 34.0 + - - -
106A HIS* 3.7 27.2 + - - -
19B LEU 3.0 10.6 + - - -
20B ILE 3.5 0.6 + - - -
21B ARG 3.2 0.4 - - - -
22B LEU* 1.3 76.4 - - - +
24B SER* 1.3 58.2 + - - +
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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