Contacts of the strand formed by residues 301 - 310 (chain A) in PDB entry 3T2E
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 LYS 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.8 4.0 - - + +
131A ALA* 3.1 4.7 - - - +
132A ASP 3.0 30.3 + - - -
273A LEU* 3.8 4.3 - - - -
274A MET* 3.2 33.9 - - + +
276A ALA* 4.0 13.9 - - + -
291A PRO* 3.8 20.9 - - + -
292A LYS 2.9 28.0 + - - +
293A MET* 3.6 19.8 - - + -
294A THR* 4.4 2.4 + - - +
298A GLY 3.2 20.6 + - - -
299A PRO* 3.1 25.1 + - - +
300A PRO* 1.3 76.4 - - - +
302A VAL* 1.3 62.6 - - - +
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Residues in contact with VAL 302 (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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50A VAL* 4.8 1.6 - - - -
129A PHE* 4.0 14.1 - - + -
130A ALA 3.3 11.9 - - - +
131A ALA* 4.1 3.1 - - + -
139A PHE* 3.9 25.8 - - + -
255A PHE* 4.0 11.4 - - + -
273A LEU* 3.8 30.1 - - + +
274A MET 2.9 7.1 + - - -
275A PRO* 3.8 17.3 - - + -
276A ALA* 2.9 26.0 + - - -
301A LYS* 1.3 77.2 - - - +
303A GLY* 1.4 71.8 + - - +
321A PHE* 3.4 10.1 - - + -
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.9 11.4 - - - +
128A ALA 3.9 0.4 - - - +
129A PHE* 3.2 9.7 - - - -
130A ALA 2.8 33.4 + - - -
276A ALA* 4.0 9.0 - - - -
278A PHE* 3.9 20.0 - - - -
291A PRO* 5.8 1.8 - - - -
302A VAL* 1.4 74.5 - - - +
304A ALA* 1.3 59.3 - - - -
321A PHE* 3.9 2.5 - - - -
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Residues in contact with ALA 304 (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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127A ILE* 4.1 7.9 - - + -
128A ALA 3.5 4.5 - - - -
129A PHE* 3.4 27.1 - - + -
252A LEU* 4.3 1.6 - - + -
276A ALA 4.9 0.2 + - - -
278A PHE* 3.7 4.1 - - - -
303A GLY* 1.3 74.3 - - - -
305A LEU* 1.4 64.3 + - - +
318A VAL 3.5 0.9 - - - +
319A ASP* 3.5 7.5 + - - +
320A LEU* 3.1 34.3 + - + -
321A PHE* 3.6 21.0 - - + -
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Residues in contact with LEU 305 (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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46A PHE* 4.2 14.6 - - + -
48A TYR* 3.6 44.6 - - + -
127A ILE* 3.4 4.0 - - - +
128A ALA* 2.9 42.9 + - + +
278A PHE* 3.6 37.5 - - + -
281A VAL* 4.2 15.0 - - + -
288A ALA* 4.3 0.7 - - + -
304A ALA* 1.4 74.6 - - - +
306A GLY* 1.3 60.6 + - - +
307A PHE* 3.5 19.7 - - + -
317A GLY* 4.3 4.0 - - - -
318A VAL 3.3 20.4 - - - +
319A ASP* 4.0 2.5 - - - +
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Residues in contact with GLY 306 (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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126A ILE 3.4 8.5 - - - -
127A ILE* 4.3 0.4 - - - -
305A LEU* 1.3 72.8 - - - +
307A PHE* 1.4 61.0 + - - -
316A GLY* 3.9 0.3 - - - -
317A GLY* 3.3 7.4 - - - -
318A VAL* 2.8 42.7 + - - +
320A LEU* 3.8 21.4 - - - +
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Residues in contact with PHE 307 (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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46A PHE* 3.8 30.5 - + + -
48A TYR* 5.4 0.2 - + - -
57A LEU* 3.4 29.4 - - + -
125A PRO* 3.4 5.2 - - - +
126A ILE* 2.9 49.1 + - + +
128A ALA* 4.3 4.9 - - + -
305A LEU* 3.5 31.4 - - + -
306A GLY* 1.4 74.7 - - - -
308A GLN* 1.3 66.4 + - - +
309A LEU* 4.5 0.2 - - + -
314A LEU* 3.9 29.8 - - + -
315A GLU 3.2 8.7 - - - +
316A GLY* 3.6 15.0 - - - -
317A GLY* 3.4 27.1 - - - -
318A VAL* 5.8 0.4 - - - -
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Residues in contact with GLN 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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123A SER* 2.9 26.5 + - - -
124A GLU 3.5 4.7 + - - -
125A PRO* 3.4 36.6 - - - +
307A PHE* 1.3 77.4 + - - +
309A LEU* 1.3 65.7 + - - +
310A HIS* 4.2 1.8 - - + -
313A TYR 3.5 0.3 - - - +
315A GLU* 2.9 42.1 + - + +
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Residues in contact with LEU 309 (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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3A VAL* 4.1 14.6 - - + -
5A VAL* 3.6 26.9 - - + -
59A THR* 4.4 7.9 - - + -
118A PHE* 4.1 6.5 - - + -
120A GLU* 3.5 15.5 - - - +
121A ARG 5.4 0.5 - - - +
123A SER* 5.7 0.5 - - - -
124A GLU* 3.1 43.4 + - + +
126A ILE* 3.6 36.8 - - + -
307A PHE* 4.5 0.2 - - + -
308A GLN* 1.3 77.2 - - - +
310A HIS* 1.3 65.1 - - - +
312A GLY* 4.7 2.2 - - - +
313A TYR 3.1 8.5 - - - +
314A LEU* 3.6 17.3 - - + -
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Residues in contact with HIS 310 (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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120A GLU* 3.6 3.6 - - - -
308A GLN* 4.2 7.0 - - + -
309A LEU* 1.3 79.7 - - - +
311A GLU* 1.3 76.3 + - + +
313A TYR* 2.8 65.3 + + + +
315A GLU* 3.4 28.5 + - + -
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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