Contacts of the helix formed by residues 293 - 308 (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 ASN 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ARG* 3.6 7.6 + - - +
286A ASP* 3.1 17.4 + - - -
290A ASN 2.8 28.8 + - - +
291A SER 2.9 10.5 + - - -
292A PHE* 1.3 74.1 - - - +
294A GLU* 1.3 53.3 + - - +
295A GLN* 3.1 11.6 + - - +
296A PHE* 2.8 31.8 + - - +
297A THR* 2.7 31.6 + - - +
73B ALA* 3.6 8.9 - - - +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASN* 1.3 72.9 - - - +
295A GLN* 1.3 60.8 + - + +
297A THR* 3.2 7.6 + - - -
298A GLU* 3.1 45.1 + - + +
17B ARG* 5.2 2.7 - - - +
20B ILE* 5.4 2.4 - - - +
21B ARG* 4.0 32.7 + - - +
26B HIS* 5.1 3.4 + - - +
27B THR* 6.2 0.2 - - - +
70B HIS* 4.7 9.6 - - - +
73B ALA* 3.6 12.7 - - + +
74B ILE* 6.1 2.0 - - + -
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Residues in contact with GLN 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG* 2.7 37.8 + - - +
293A ASN* 3.1 8.2 + - - +
294A GLU* 1.3 78.1 - - + +
296A PHE* 1.3 62.6 + - - +
298A GLU* 3.6 17.7 - - - +
299A LEU 3.7 1.2 + - - -
340A PRO* 3.3 22.6 + - - +
341A TYR* 2.6 51.6 + - + +
342A ASP* 3.2 21.5 + - - +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG* 4.6 3.6 - - + +
285A ASP 4.4 6.5 - - - -
286A ASP* 3.7 36.3 - - + +
291A SER* 3.5 29.8 - - - +
293A ASN* 2.8 19.1 + - - +
295A GLN* 1.3 74.9 - - - +
297A THR* 1.3 60.1 + - - +
300A ASP* 3.0 41.5 + - + +
311A LEU* 3.3 47.1 - - + +
312A ARG 4.3 13.7 - - - -
313A THR* 4.5 7.0 - - + -
341A TYR* 4.4 0.9 - - - -
69B ARG* 3.4 37.2 - - - -
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Residues in contact with THR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A SER 4.5 7.0 - - - +
293A ASN 2.7 23.7 + - - +
294A GLU* 3.2 5.9 + - - -
296A PHE* 1.3 76.1 - - - +
298A GLU* 1.3 64.7 + - - -
300A ASP* 4.2 4.0 - - - -
301A LEU* 3.0 32.9 + - - +
66B ARG 4.9 1.3 - - - +
69B ARG* 3.8 19.7 - - + +
70B HIS* 3.0 59.7 - - + +
73B ALA* 4.8 0.2 - - + -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 3.1 33.8 + - + +
295A GLN* 3.6 15.7 - - - +
297A THR* 1.3 77.0 + - - +
299A LEU* 1.3 62.2 + - - +
301A LEU* 4.6 1.0 - - - +
302A ARG* 3.4 26.5 + - - +
340A PRO 5.2 1.4 - - - +
341A TYR* 3.6 21.5 - - + -
600A ERT 3.6 36.7 - - - +
20B ILE* 4.0 17.5 - - - +
26B HIS* 3.3 39.2 + - + +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PHE* 4.0 16.6 - - + -
255A LEU* 3.7 26.9 - - + -
284A ARG* 4.8 2.9 - - + -
295A GLN 3.7 0.6 + - - +
296A PHE 3.6 0.8 + - - -
297A THR 3.2 0.4 - - - -
298A GLU* 1.3 78.8 - - - +
300A ASP* 1.3 64.6 + - - +
301A LEU 3.2 1.8 - - - -
302A ARG* 3.3 5.3 + - + +
303A MET* 3.0 30.1 + - + +
311A LEU* 3.9 17.7 - - + -
341A TYR* 3.5 29.8 - - + +
600A ERT 3.7 56.1 - - + +
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.0 33.0 + - + +
297A THR* 3.9 5.3 - - - +
299A LEU* 1.3 77.3 - - - +
301A LEU* 1.3 61.3 + - - +
303A MET* 3.5 3.7 - - - +
304A LEU 3.1 12.0 + - - -
310A ALA* 3.5 1.9 - - - +
311A LEU* 3.1 36.8 + - + +
66B ARG* 2.6 75.4 + - - +
69B ARG* 4.6 4.8 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.6 15.2 - - + -
122A LEU* 5.0 10.5 - - + +
126A ILE* 5.2 1.1 - - + -
297A THR* 3.0 21.0 + - - +
298A GLU 4.6 1.6 - - - +
300A ASP* 1.3 78.2 - - - +
302A ARG* 1.3 63.8 + - - +
303A MET 3.2 1.1 - - - -
304A LEU* 3.6 23.4 - - + +
305A VAL* 3.2 25.8 + - - +
26B HIS* 4.4 9.4 - - + -
30B VAL* 3.8 28.0 - - + -
66B ARG* 4.1 27.8 - - + +
67B LEU* 4.6 5.4 - - + +
70B HIS* 3.9 22.7 - - + +
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.8 11.5 - - - +
105A TRP* 4.3 7.3 + - - -
106A HIS* 6.0 2.0 - - - -
112A VAL* 3.7 16.7 - - - +
116A ASP* 2.6 38.5 + - - -
119A PHE* 3.7 17.4 - - + -
298A GLU 3.4 15.7 + - - +
299A LEU* 3.3 9.5 + - + +
301A LEU* 1.3 76.6 - - - +
303A MET* 1.3 60.9 + - - +
306A PHE* 2.8 58.0 + - + -
600A ERT 2.6 77.2 + - - +
24B SER* 5.9 1.8 - - - +
25B LEU 5.8 0.4 - - - +
26B HIS* 5.5 5.5 + - - +
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Residues in contact with MET 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 3.2 33.7 - - + +
256A ASN* 2.9 51.8 - - - +
299A LEU* 3.0 19.0 + - + +
300A ASP 3.5 9.9 - - - +
302A ARG* 1.3 78.8 - - - +
304A LEU* 1.3 59.2 + - - +
307A LEU* 3.1 29.3 + - + +
308A GLY 3.0 9.4 + - - -
309A GLY 2.9 20.8 + - - -
310A ALA* 3.7 18.6 - - - +
311A LEU 5.2 0.2 - - - +
600A ERT 4.4 20.4 - - - -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 4.5 4.9 - - + -
125A ALA* 4.2 20.4 - - + +
126A ILE* 4.0 26.7 - - + -
129A GLY* 3.9 29.4 - - - +
131A PRO* 3.4 11.6 - - - +
300A ASP 3.1 7.3 + - - +
301A LEU* 3.6 23.1 - - + +
302A ARG 3.3 0.2 - - - -
303A MET* 1.3 74.7 - - - +
305A VAL* 1.3 60.8 + - - +
308A GLY* 3.1 22.4 + - - +
309A GLY 3.8 7.6 + - - -
63B ALA* 4.7 6.7 - - + -
66B ARG* 3.3 39.3 - - + +
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.3 42.8 - - - +
119A PHE* 4.0 13.9 - - + +
122A LEU* 4.2 19.7 - - + -
125A ALA* 3.8 24.7 - - + -
131A PRO* 4.4 0.4 - - - -
132A THR* 3.0 30.3 + - - +
133A TYR 3.4 7.3 + - - -
301A LEU 3.2 15.4 + - - +
304A LEU* 1.3 79.7 - - + +
306A PHE* 1.3 75.3 + - + +
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 4.2 4.7 - - + -
115A ALA* 3.1 50.5 - - + -
116A ASP* 3.5 26.5 - - - -
118A SER* 4.1 2.0 - - - -
119A PHE* 4.3 3.1 - + - -
131A PRO* 3.9 4.6 - - - +
133A TYR* 3.5 21.8 - + + +
141A PHE* 3.7 21.6 + + + +
302A ARG* 2.8 46.0 + - + +
303A MET* 5.4 0.2 - - - -
305A VAL* 1.3 94.3 - - + +
307A LEU* 1.3 70.6 + - + +
600A ERT 3.6 32.8 - + - -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 4.9 2.9 + - - -
131A PRO* 3.7 11.8 - - - +
140A PRO* 6.4 0.4 - - + -
141A PHE* 3.7 41.3 - - + +
142A TYR* 4.3 13.5 - - + +
256A ASN* 3.5 32.0 - - + +
257A TRP* 5.7 5.7 - - + -
258A PRO* 4.8 4.7 - - - +
303A MET* 3.1 32.7 + - + +
305A VAL 3.5 0.2 - - - -
306A PHE* 1.3 95.8 - - + +
308A GLY* 1.3 62.0 + - - +
309A GLY 3.5 1.0 + - - +
600A ERT 4.0 13.0 - - + -
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Residues in contact with GLY 308 (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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129A GLY 4.9 8.0 - - - +
130A ARG* 4.6 5.6 + - - -
131A PRO* 3.5 18.0 - - - +
258A PRO* 3.6 26.8 - - - +
303A MET 3.0 3.0 + - - -
304A LEU* 3.1 17.7 + - - -
307A LEU* 1.3 77.7 - - - +
309A GLY* 1.3 63.5 + - - +
66B ARG* 5.0 2.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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