Contacts of the helix formed by residues 60 - 74 (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 ARG 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE 3.2 9.4 + - - +
127A ARG 3.5 12.1 + - - +
128A THR* 3.4 22.6 + - - +
129A GLY* 3.6 22.2 + - - +
54B ALA* 4.5 0.4 - - - -
59B THR* 1.3 72.9 - - - +
61B PRO* 1.3 70.7 - - + +
62B GLU* 2.9 41.7 + - - +
63B ALA* 3.0 16.7 + - + +
64B LEU* 3.1 10.3 + - - +
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Residues in contact with PRO 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.4 19.5 - - + +
51B LYS* 5.1 15.7 - - + -
54B ALA* 3.8 22.2 - - + -
59B THR 3.4 8.7 - - - +
60B ARG* 1.3 84.9 - - + -
62B GLU* 1.3 71.4 + - - +
64B LEU* 3.5 1.4 + - + -
65B LEU* 3.0 24.9 + - - +
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Residues in contact with GLU 62 (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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60B ARG* 2.9 45.2 + - - +
61B PRO* 1.3 93.9 - - - +
63B ALA* 1.3 62.6 + - - +
65B LEU* 3.6 11.3 + - - +
66B ARG* 3.3 25.7 + - - +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 3.9 16.4 - - - +
126A ILE* 3.6 30.2 - - + +
129A GLY* 4.2 13.2 - - - -
304A LEU* 4.7 8.5 - - + -
60B ARG* 3.0 11.2 + - - +
62B GLU* 1.3 79.6 - - - +
64B LEU* 1.3 63.6 + - - +
66B ARG* 3.1 23.2 + - - +
67B LEU 3.1 10.4 + - - -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.0 17.7 - - + +
37B LEU* 4.5 4.9 - - + -
39B LEU* 4.4 16.6 - - + -
50B VAL* 4.0 7.2 - - + +
53B LEU* 3.7 17.0 - - + +
54B ALA* 3.3 39.5 - - + +
57B THR* 4.0 3.4 - - - +
59B THR* 3.6 17.3 - - - +
60B ARG 3.1 8.8 + - - +
61B PRO* 3.6 9.4 - - + +
63B ALA* 1.3 77.4 - - - +
65B LEU* 1.3 56.0 + - - +
67B LEU* 3.3 17.8 + - + +
68B ILE* 3.0 42.7 + - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A HIS* 4.9 14.8 - - + +
292A PHE* 5.0 10.5 - - + -
316A LYS* 5.3 7.6 - - - +
50B VAL* 4.3 23.7 - - + +
61B PRO 3.0 17.3 + - - +
62B GLU* 3.8 9.6 - - - +
63B ALA 3.3 0.4 - - - -
64B LEU* 1.3 76.7 - - - +
66B ARG* 1.3 57.6 + - - +
68B ILE* 3.3 9.6 + - + +
69B ARG* 2.8 44.3 + - + +
85B PHE* 4.5 20.0 - - + -
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 5.3 0.8 + - - -
297A THR* 4.9 1.2 - - - +
300A ASP* 2.6 62.8 + - - +
301A LEU* 4.1 18.5 - - + +
304A LEU* 3.3 35.7 - - + +
308A GLY 5.0 1.8 + - - -
309A GLY 3.1 26.2 + - - -
310A ALA* 3.8 10.6 - - - +
311A LEU 5.7 0.2 - - - -
62B GLU 3.3 17.8 + - - +
63B ALA* 3.1 13.4 + - - +
65B LEU* 1.3 75.3 - - - +
67B LEU* 1.3 64.3 + - - +
69B ARG* 3.3 36.6 - - - +
70B HIS* 3.5 6.2 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.5 24.0 - - + -
126A ILE* 3.9 20.8 - - + +
301A LEU* 4.6 7.0 - - + +
30B VAL* 3.9 20.8 - - + +
33B THR* 3.4 28.5 - - - +
34B ALA 4.5 4.5 - - - +
37B LEU* 4.2 14.6 - - + -
39B LEU* 4.2 25.1 - - + -
63B ALA 3.1 3.4 + - - +
64B LEU* 3.6 15.0 - - + +
66B ARG* 1.3 77.2 - - - +
68B ILE* 1.3 62.7 + - - +
70B HIS* 3.3 6.2 + - - +
71B LEU* 3.1 28.8 + - + +
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Residues in contact with ILE 68 (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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39B LEU* 4.7 7.2 - - + -
50B VAL* 4.5 15.7 - - + -
53B LEU* 4.3 21.3 - - + -
64B LEU* 3.0 40.4 + - + +
65B LEU* 3.6 10.5 - - + +
67B LEU* 1.3 74.4 - - - +
69B ARG* 1.3 65.9 + - - +
71B LEU* 3.3 12.5 + - + +
72B VAL* 3.1 21.5 + - - +
77B LEU* 4.3 18.8 - - + -
85B PHE* 3.6 44.0 - - + -
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Residues in contact with ARG 69 (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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288A HIS* 4.0 22.2 + - - -
291A SER* 3.4 31.2 + - - +
292A PHE* 3.6 36.1 - - + -
296A PHE* 3.4 33.8 - - - -
297A THR* 3.8 11.1 - - + +
300A ASP* 4.6 3.2 + - - -
311A LEU 5.3 3.2 + - - -
313A THR* 4.1 10.1 - - - +
316A LYS* 3.8 21.6 - - - +
65B LEU* 2.8 25.6 + - + +
66B ARG* 3.3 38.7 - - - +
68B ILE* 1.3 78.3 - - - +
70B HIS* 1.3 62.1 + - - +
72B VAL* 3.2 4.5 + - - +
73B ALA* 3.2 16.3 + - - +
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Residues in contact with HIS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 4.7 9.5 - - - +
297A THR* 3.0 38.1 - - + +
301A LEU* 3.9 15.9 - - + -
26B HIS* 3.5 21.7 + + - -
27B THR* 3.1 35.4 + - + -
30B VAL* 3.5 22.4 - - + +
66B ARG 3.5 2.0 + - - +
67B LEU 3.3 7.4 + - - +
68B ILE 3.3 0.2 - - - -
69B ARG* 1.3 76.4 - - - +
71B LEU* 1.3 63.5 + - - +
73B ALA* 3.3 6.4 + - + +
74B ILE* 3.1 44.5 + - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.5 23.5 - - + +
31B VAL* 4.6 0.2 - - - -
34B ALA* 4.0 20.0 - - + -
39B LEU* 3.6 31.9 - - + -
67B LEU* 3.1 25.3 + - + +
68B ILE* 3.3 10.5 + - - +
70B HIS* 1.3 73.7 - - - +
72B VAL* 1.3 60.8 + - - +
74B ILE* 3.7 7.2 - - + +
75B GLY 3.4 2.1 + - - -
76B LEU* 3.0 50.1 + - + -
77B LEU* 3.0 30.7 + - + +
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Residues in contact with VAL 72 (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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292A PHE* 3.8 27.6 - - + +
68B ILE 3.1 16.9 + - - +
69B ARG 3.4 7.9 - - - +
70B HIS 3.2 0.2 - - - -
71B LEU* 1.3 74.8 - - - +
73B ALA* 1.3 68.4 + - - +
75B GLY* 3.0 15.4 + - - -
77B LEU* 3.2 28.0 - - + +
78B GLU* 4.1 7.9 - - + -
79B GLU* 4.9 1.6 - - + +
85B PHE* 3.9 29.6 - - + -
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Residues in contact with ALA 73 (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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292A PHE 3.9 8.0 + - - +
293A ASN* 3.6 38.8 - - - +
294A GLU* 3.6 10.3 - - + +
69B ARG 3.2 7.2 + - - +
70B HIS* 3.3 14.8 + - + +
72B VAL* 1.3 79.1 - - - +
74B ILE* 1.3 59.9 + - + +
75B GLY* 3.6 0.3 + - - -
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Residues in contact with ILE 74 (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* 3.6 31.2 - - + +
294A GLU* 6.1 2.7 - - + -
21B ARG* 5.6 2.9 + - - +
27B THR* 4.0 20.6 - - + +
30B VAL* 4.8 0.9 - - + -
31B VAL* 3.9 27.8 - - + -
70B HIS* 3.1 47.3 + - + +
71B LEU* 3.7 17.9 - - + +
73B ALA* 1.3 77.3 - - + +
75B GLY* 1.3 58.8 + - - +
76B LEU* 4.2 13.7 - - + +
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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