Contacts of the strand formed by residues 326 - 335 (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 LEU 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 4.1 14.8 - - + +
270A ALA* 4.1 17.0 - - + -
273A LEU* 4.9 1.3 - - + -
279A ILE* 3.9 28.0 - - + -
318A ASP 5.1 0.2 - - - +
321A ALA* 2.9 30.8 + - + +
322A ALA* 3.5 8.7 + - - +
324A ALA* 3.8 21.8 - - + +
325A GLY* 1.3 86.1 - - - +
327A VAL* 1.3 66.0 + - - +
348A LEU* 3.9 21.8 - - + -
349A ALA* 3.2 28.5 - - - +
350A PRO* 3.9 7.0 - - + -
351A ALA* 4.0 6.7 - - - +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA* 4.4 1.6 - - - -
326A LEU* 1.3 76.7 - - - +
328A VAL* 1.3 69.2 + - - +
329A GLU* 3.4 6.2 + - - +
348A LEU* 3.3 7.4 - - - -
349A ALA* 2.9 46.9 + - + +
350A PRO 3.7 13.7 - - - +
351A ALA* 4.4 13.2 - - + -
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Residues in contact with VAL 328 (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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314A ARG* 5.4 3.8 - - - -
317A TRP* 4.0 19.5 - - + +
318A ASP* 3.8 25.4 + - - +
321A ALA* 3.9 17.2 - - + +
327A VAL* 1.3 73.8 - - - +
329A GLU* 1.3 63.1 + - - +
330A GLU 4.3 4.3 - - - +
331A VAL* 4.1 26.2 - - + -
346A LEU* 4.3 7.2 - - + -
347A VAL 3.9 4.5 - - - +
348A LEU* 3.8 23.3 - - + -
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Residues in contact with GLU 329 (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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278A ARG* 2.7 39.9 + - - -
327A VAL* 3.4 11.8 + - + +
328A VAL* 1.3 73.2 - - - +
330A GLU* 1.3 67.0 + - + +
347A VAL* 2.9 27.4 + - + +
348A LEU 5.0 0.2 - - - +
349A ALA* 3.5 18.3 - - + +
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Residues in contact with GLU 330 (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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173A ALA 5.2 1.0 - - - +
174A TYR* 5.5 3.6 - - - -
328A VAL* 3.7 2.4 - - - +
329A GLU* 1.3 86.9 - - + +
331A VAL* 1.3 68.0 + - - +
332A ARG* 3.6 39.2 + - - +
345A LEU 3.7 1.4 - - - +
346A LEU* 3.6 0.7 - - - -
347A VAL* 3.1 51.8 + - + +
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Residues in contact with VAL 331 (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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285A ASP* 4.2 8.1 - - - +
314A ARG* 3.6 57.0 + - - +
328A VAL* 4.1 16.8 - - + -
330A GLU* 1.3 83.0 - - - +
332A ARG* 1.3 75.5 + - - +
333A GLN* 5.4 1.1 - - + -
344A SER* 4.5 3.6 - - - -
345A LEU 3.5 8.3 - - - +
346A LEU* 4.2 14.1 - - + -
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Residues in contact with ARG 332 (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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173A ALA* 3.1 49.5 + - - +
330A GLU* 3.6 30.6 + - - +
331A VAL* 1.3 79.3 - - - +
333A GLN* 1.3 70.2 + - - +
334A LEU* 4.9 10.1 - - + +
344A SER* 3.4 5.0 - - - -
345A LEU* 3.1 46.7 + - + +
347A VAL* 6.0 1.3 - - - +
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Residues in contact with GLN 333 (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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284A ARG* 4.0 10.3 + - - +
285A ASP* 3.5 21.0 + - - -
286A ASP* 3.3 24.9 + - - +
314A ARG* 4.4 13.6 - - - +
331A VAL* 5.4 0.4 - - + -
332A ARG* 1.3 80.9 - - - +
334A LEU* 1.3 67.9 + - - +
335A PRO* 4.8 0.9 - - - +
342A ASP* 5.1 14.7 - - + +
343A LEU 3.2 9.2 - - - +
344A SER* 4.2 6.4 + - - +
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Residues in contact with LEU 334 (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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169A ALA* 3.8 25.6 - - + +
170A PRO* 3.9 32.5 - - + -
173A ALA* 4.4 14.6 - - + -
282A HIS* 5.9 2.5 - - + +
332A ARG* 4.3 8.9 + - + +
333A GLN* 1.3 81.4 - - - +
335A PRO* 1.3 74.5 - - + +
342A ASP* 3.5 3.9 - - - -
343A LEU* 2.7 46.9 + - + +
344A SER 6.0 0.4 - - - -
345A LEU* 4.6 15.7 - - + +
7B ALA* 5.1 3.8 - - + -
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Residues in contact with PRO 335 (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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169A ALA* 4.9 5.0 - - - +
333A GLN 4.8 0.9 - - - +
334A LEU* 1.3 96.1 - - + +
336A SER* 1.3 63.7 + - - +
337A PRO* 3.7 4.7 - - - +
342A ASP* 3.6 13.7 - - - +
343A LEU* 4.0 3.2 - - - +
7B ALA* 3.5 38.8 - - + +
8B ALA 4.6 0.6 - - - +
9B ARG* 3.7 48.7 - - + +
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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