Contacts of the strand formed by residues 435 - 445 (chain B) in PDB entry 1NDM
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 SER 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433B GLY* 4.0 9.9 - - - -
434B SER* 1.3 78.1 - - - +
436B VAL* 1.3 59.6 + - - +
437B THR* 5.3 2.2 - - - +
490B THR* 4.0 17.4 - - - +
491B VAL 3.4 14.4 - - - -
492B THR* 4.3 2.0 - - - +
493B SER* 2.9 11.7 + - - +
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Residues in contact with VAL 436 (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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426B PRO* 4.3 23.3 - - + -
435B SER* 1.3 76.1 - - - +
437B THR* 1.3 74.0 + - - +
438B LEU* 4.3 12.7 - - + +
489B VAL 3.8 0.5 - - - +
490B THR* 3.3 1.2 - - - -
491B VAL* 2.7 57.8 + - + +
492B THR 4.3 0.2 - - - +
493B SER* 3.8 21.3 - - - +
497B TRP* 4.4 15.3 - - + -
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Residues in contact with THR 437 (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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114A THR* 5.1 12.3 - - + -
116A SER* 3.0 32.7 + - - +
118A PHE* 3.3 17.7 - - - -
135A PHE* 5.1 2.3 - - - +
137A ASN* 5.6 4.9 - - - +
426B PRO* 4.6 3.1 - - - +
435B SER* 5.3 1.8 - - - +
436B VAL* 1.3 80.3 - - - +
438B LEU* 1.3 68.6 - - - +
488B SER* 5.3 4.5 - - - -
489B VAL 3.2 5.8 - - - -
490B THR* 2.9 38.4 - - + +
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Residues in contact with LEU 438 (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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118A PHE* 4.1 4.9 - - - -
135A PHE* 4.3 0.9 - - - -
424B LEU 3.7 3.4 - - - -
426B PRO* 3.3 35.4 - - + -
436B VAL* 4.3 15.5 - - + -
437B THR* 1.3 79.4 - - - +
439B GLY* 1.3 59.8 + - - +
488B SER* 3.2 8.5 - - - -
489B VAL* 2.8 44.7 + - + +
491B VAL* 4.4 2.2 - - + -
497B TRP* 4.2 22.2 - - + -
503B ILE* 3.8 27.6 - - + -
521B ILE* 3.6 32.3 - - + -
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Residues in contact with GLY 439 (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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135A PHE* 4.1 5.6 - - - -
424B LEU* 2.7 54.6 + - - +
438B LEU* 1.3 78.1 - - - +
440B CYS* 1.3 58.3 + - - -
455B TRP* 3.6 5.2 - - - -
487B SER 3.2 10.1 - - - -
521B ILE* 3.4 12.1 - - - +
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Residues in contact with CYS 440 (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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421B VAL* 3.8 20.0 - - - -
422B TYR 3.5 8.1 - - - -
423B PRO* 4.9 0.7 - - - -
424B LEU* 3.9 4.3 - - - +
439B GLY* 1.3 73.2 - - - +
441B LEU* 1.3 62.7 + - - +
442B VAL* 4.1 2.2 + - - -
452B LEU* 4.2 10.5 - - + +
455B TRP* 3.5 15.9 - - + -
486B SER* 3.2 6.2 - - - -
487B SER 2.9 29.7 + - - +
506B CYS* 2.0 50.0 - - + -
508B VAL* 4.4 1.3 - - - -
519B LYS* 5.2 0.4 - - - -
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Residues in contact with LEU 441 (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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124A GLN* 4.6 4.9 - - - +
131A SER* 3.9 30.7 - - - +
133A VAL* 4.2 15.7 - - + -
178A THR* 5.1 5.4 - - + +
420B SER 3.5 1.6 - - - +
421B VAL* 3.4 5.2 - - - +
422B TYR* 2.9 64.6 + - + +
424B LEU* 4.2 15.7 - - + +
440B CYS* 1.3 74.3 - - - +
442B VAL* 1.3 61.6 + - - +
443B LYS* 4.4 7.9 - - + -
484B THR* 3.8 20.4 - - + -
485B LEU 3.5 13.7 - - - +
486B SER* 4.1 11.0 - - - -
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B PRO* 3.4 32.3 - - + -
420B SER 3.5 3.8 - - - +
421B VAL* 4.6 3.1 - - + -
440B CYS* 4.7 2.5 - - - +
441B LEU* 1.3 74.6 - - - +
443B LYS* 1.3 59.9 + - - +
445B TYR* 3.6 15.4 - - + -
450B VAL* 4.5 5.2 - - + -
452B LEU* 4.1 7.4 - - + -
484B THR* 3.2 4.9 - - - +
485B LEU* 2.7 65.1 + - + +
508B VAL* 3.7 36.3 - - + -
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Residues in contact with LYS 443 (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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124A GLN* 3.9 21.6 - - - +
131A SER* 3.9 15.3 - - - +
180A THR* 4.2 9.2 - - - +
419B PRO* 3.6 1.3 - - - +
420B SER* 2.8 43.6 + - - +
422B TYR* 4.5 12.3 - - + +
441B LEU* 3.8 13.0 + - + -
442B VAL* 1.3 75.5 - - - +
444B GLY* 1.3 67.3 + - - +
445B TYR* 3.7 1.8 - - - -
477B GLN* 3.5 30.4 + - - +
478B SER* 6.4 0.2 - - - -
483B TYR 4.1 0.4 - - - -
484B THR* 3.4 18.8 - - + +
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Residues in contact with GLY 444 (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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417B THR* 3.2 24.6 - - - +
418B ALA 3.4 6.1 - - - +
443B LYS* 1.3 83.5 - - - +
445B TYR* 1.3 57.5 + - - -
482B LEU* 3.7 26.6 - - - +
483B TYR 3.0 13.0 + - - -
484B THR* 3.7 1.0 + - - -
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Residues in contact with TYR 445 (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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417B THR* 3.1 15.0 - - - +
419B PRO* 3.4 22.0 - - + -
442B VAL* 3.6 41.5 - - + -
444B GLY* 1.3 77.0 - - - +
446B PHE* 1.3 65.8 + - - +
447B PRO 3.7 16.2 - - - -
448B GLU* 4.3 13.2 + - + -
449B PRO* 5.5 0.2 - - - +
450B VAL* 3.5 35.6 + - + +
474B ALA* 3.3 25.6 - - - +
482B LEU* 3.8 2.1 - - - -
483B TYR* 2.9 57.4 + + + +
484B THR* 4.1 1.8 - - - -
485B LEU* 3.9 6.1 - - - +
510B HIS* 4.0 2.5 - - - +
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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