Contacts of the strand formed by residues 337 - 348 (chain A) in PDB entry 3L2V
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 TRP 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.0 36.6 + - - +
102A THR 4.3 1.3 - - - -
103A ASN 3.1 27.5 + - - -
104A ALA* 3.9 9.4 - - + +
105A SER* 4.6 12.3 - - - -
324A GLN* 3.6 21.3 - - - +
325A GLU 3.6 7.0 - - - -
326A ARG* 3.4 68.2 - - + -
327A VAL* 3.9 8.5 - - - +
335A PRO* 3.2 8.1 - - - +
336A ARG* 1.3 92.6 - - + +
338A HIS* 1.3 69.1 + - - +
368A ASN 3.9 4.0 - - - -
369A LEU 4.1 4.0 - - - -
370A LYS* 3.6 42.4 - - + -
802A GOL 5.4 0.7 + - - -
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Residues in contact with HIS 338 (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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101A ILE* 3.7 2.4 - - - +
324A GLN* 2.6 34.7 + - - +
325A GLU* 2.8 43.6 + - + +
326A ARG 3.5 14.6 + - - -
327A VAL* 3.7 25.3 - - + +
328A ALA* 4.3 5.4 + - + +
337A TRP* 1.3 74.9 - - - +
339A LYS* 1.3 61.6 + - - +
341A SER* 6.0 0.2 - - - +
357A HIS* 3.5 31.2 + + + -
802A GOL 2.2 40.4 + - - +
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Residues in contact with LYS 339 (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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97A GLN* 4.0 16.6 - - - +
101A ILE* 4.0 8.8 - - + +
324A GLN* 3.8 5.0 - - - +
338A HIS* 1.3 84.0 - - - +
340A PRO* 1.4 81.8 - - + +
341A SER* 3.6 7.4 + - - -
357A HIS* 6.1 0.6 - - + -
358A LEU* 6.0 5.2 - - + -
802A GOL 2.5 36.2 + - - +
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Residues in contact with PRO 340 (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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97A GLN* 4.8 12.3 - - - +
100A LEU* 4.8 13.2 - - + -
101A ILE* 5.1 2.2 - - + -
322A LEU* 4.3 22.0 - - + -
324A GLN* 3.5 18.4 - - + +
339A LYS* 1.4 92.3 - - + +
341A SER* 1.3 62.0 + - - +
356A ASP 5.9 0.3 - - - -
358A LEU* 5.2 8.7 - - - +
372A THR* 3.8 25.4 - - + +
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Residues in contact with SER 341 (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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321A GLN 3.4 1.4 - - - +
322A LEU* 3.7 4.7 - - - +
323A VAL* 2.9 42.1 + - - +
324A GLN* 4.4 3.3 - - - -
325A GLU* 4.6 3.1 + - - +
338A HIS* 6.0 0.2 - - - +
339A LYS 3.9 6.5 + - - -
340A PRO* 1.3 75.5 - - - +
342A THR* 1.3 64.8 + - - +
354A ILE* 4.0 18.9 - - - +
355A LEU 3.1 20.6 - - - -
356A ASP* 3.9 14.7 - - - +
357A HIS* 6.1 0.3 - - - -
369A LEU* 6.0 0.2 - - - +
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Residues in contact with THR 342 (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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320A GLY* 3.8 25.4 - - - -
321A GLN 3.5 7.0 - - - +
322A LEU* 4.2 10.9 - - + +
323A VAL* 5.4 0.2 - - - -
341A SER* 1.3 79.3 - - - +
343A VAL* 1.3 69.9 + - - +
344A LEU* 3.3 10.6 + - + +
354A ILE* 3.3 6.8 - - - -
355A LEU* 3.2 35.1 + - - +
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Residues in contact with VAL 343 (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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317A PRO* 4.7 5.8 - - + -
318A VAL 3.4 27.4 - - - +
319A VAL* 3.6 10.8 - - - +
320A GLY* 3.0 23.0 + - - +
321A GLN* 3.2 10.6 + - + +
323A VAL* 3.7 31.6 - - + -
342A THR* 1.3 73.5 - - - +
344A LEU* 1.3 63.3 + - - +
345A LYS 3.9 4.5 - - - +
346A VAL* 3.8 21.3 - - + -
352A VAL* 3.9 21.1 - - + -
353A VAL 3.8 3.8 - - - -
354A ILE* 4.4 2.2 - - + -
369A LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 344 (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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319A VAL* 3.4 21.0 - - - +
342A THR* 3.3 8.9 + - + +
343A VAL* 1.3 75.3 - - - +
345A LYS* 1.3 59.4 + - + +
353A VAL* 2.7 24.3 + - + +
354A ILE 4.1 2.2 - - - -
355A LEU* 3.6 48.7 - - + +
361A ASN* 3.9 28.9 - - - +
1C A 6.3 0.4 - - - +
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Residues in contact with LYS 345 (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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319A VAL* 5.1 3.1 - - - -
343A VAL* 3.9 0.6 - - - +
344A LEU* 1.3 80.3 - - + +
346A VAL* 1.3 65.3 + - - +
347A LEU* 3.8 11.7 - - + -
352A VAL* 3.6 6.8 - - - +
353A VAL* 3.0 36.2 + - + +
1C A 4.7 14.1 - - - +
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Residues in contact with VAL 346 (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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317A PRO* 3.5 34.3 - - + +
319A VAL* 4.1 19.4 - - + +
343A VAL* 3.8 20.0 - - + -
345A LYS* 1.3 75.2 - - - +
347A LEU* 1.3 64.9 + - - +
348A ASN* 3.4 25.5 - - - +
349A PRO* 4.6 4.9 - - + -
351A THR 4.0 4.5 - - - +
352A VAL* 4.6 1.8 - - + +
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Residues in contact with LEU 347 (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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345A LYS* 3.8 8.0 - - + -
346A VAL* 1.3 72.9 - - - +
348A ASN* 1.3 62.4 + - - +
351A THR* 3.1 19.6 + - + +
352A VAL 4.9 0.2 - - - -
353A VAL* 3.8 21.5 - - + +
363A THR* 3.6 31.0 - - + +
1C A 3.8 39.7 - - + +
2C T 3.0 36.9 + - + +
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Residues in contact with ASN 348 (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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113A LEU* 3.5 19.4 - - + +
317A PRO* 4.8 0.5 - - - +
346A VAL* 3.3 14.4 - - - +
347A LEU* 1.3 77.9 - - - +
349A PRO* 1.4 65.5 - - + +
350A ARG* 2.6 23.2 + - - -
351A THR* 2.5 61.8 + - - +
2C T 4.6 9.8 + - + +
3C T 3.2 24.0 + - - -
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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