Contacts of the helix formed by residues 555 - 570 (chain A) in PDB entry 4N78
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 555 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A GLY 3.9 0.8 + - - -
554A PRO* 1.3 76.6 - - - +
556A SER* 1.3 66.9 + - - +
557A THR* 3.1 20.8 + - - -
558A GLN* 3.0 28.5 + - - +
559A LEU* 3.0 19.8 + - - +
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Residues in contact with SER 556 (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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554A PRO 3.9 0.6 + - - -
555A SER* 1.3 72.3 - - - +
557A THR* 1.3 66.0 + - - +
559A LEU* 3.4 5.1 + - - +
560A TYR* 3.0 31.3 + - - +
603A THR* 6.5 0.4 - - - -
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Residues in contact with THR 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A SER* 3.1 13.5 + - - -
556A SER* 1.3 86.6 + - - +
558A GLN* 1.3 61.2 + - - +
560A TYR* 3.9 4.9 - - - +
561A MET* 2.9 43.0 + - - +
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Residues in contact with GLN 558 (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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484A LEU* 6.0 0.2 - - - -
517A THR* 3.2 34.5 + - + +
518A VAL* 3.8 26.6 + - + +
554A PRO* 3.4 17.2 - - + +
555A SER* 3.0 38.9 + - - +
557A THR* 1.3 82.9 + - - +
559A LEU* 1.3 57.7 + - - +
561A MET* 4.0 0.9 - - - +
562A VAL* 3.1 35.7 + - - +
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Residues in contact with LEU 559 (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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480A VAL* 5.8 0.2 - - + -
484A LEU* 5.4 9.4 - - + -
554A PRO* 4.3 21.7 - - + +
555A SER 3.0 14.5 + - - +
556A SER* 3.9 5.6 - - - +
558A GLN* 1.3 74.2 - - - +
560A TYR* 1.3 65.9 + - - +
562A VAL* 3.5 6.2 + - + -
563A ARG* 3.0 49.3 + - + +
595A PHE* 5.5 2.0 - - + -
599A SER* 4.7 5.6 - - - +
602A TYR* 3.7 39.9 - - + -
603A THR* 3.5 26.9 - - - +
606A ILE* 5.9 2.9 - - + -
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Residues in contact with TYR 560 (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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59A TYR* 5.1 2.5 - - + -
62A GLN* 4.0 14.8 + - + +
63A ALA* 3.7 30.7 + - + -
66A HIS* 3.3 33.3 + + + +
154A SER* 4.1 7.7 + - - -
156A ALA* 4.3 17.0 - - + -
556A SER 3.0 19.1 + - - +
557A THR* 3.9 5.8 - - - +
559A LEU* 1.3 78.2 - - - +
561A MET* 1.3 66.7 + - + +
563A ARG* 4.0 4.2 - - - +
564A THR* 2.5 58.8 + - + +
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Residues in contact with MET 561 (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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56A ILE* 4.0 27.1 - - + +
59A TYR* 3.5 45.1 - - + +
60A ILE* 4.5 9.0 - - + -
63A ALA* 5.2 2.5 - - - -
517A THR* 5.0 10.5 - - + +
557A THR* 2.9 31.3 + - - +
558A GLN* 4.0 4.3 - - - +
560A TYR* 1.3 88.4 - - + +
562A VAL* 1.3 60.0 + - - +
564A THR* 3.4 2.9 + - - -
565A MET* 2.9 51.7 + - + +
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Residues in contact with VAL 562 (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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484A LEU* 4.4 11.9 - - + -
487A PHE* 5.5 1.6 - - + -
514A ILE* 4.1 26.6 - - + +
517A THR* 5.2 2.2 - - + -
518A VAL* 3.4 28.5 - - + -
558A GLN 3.1 22.6 + - - +
559A LEU* 3.9 6.1 - - + +
561A MET* 1.3 77.2 - - - +
563A ARG* 1.3 59.3 - - + +
565A MET* 3.3 8.3 + - + +
566A LEU* 2.9 49.3 + - + +
595A PHE* 4.2 14.8 - - + -
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Residues in contact with ARG 563 (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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155A GLU* 5.1 4.4 + - - +
248A TYR* 5.3 1.0 + - - -
559A LEU* 3.0 37.9 + - + +
560A TYR* 4.0 4.0 - - - +
562A VAL* 1.3 80.4 - - + +
564A THR* 1.3 58.0 + - - +
566A LEU* 3.4 3.5 + - - -
567A GLU* 2.9 36.4 + - - +
595A PHE* 5.4 2.2 - - + -
596A HIS* 2.6 63.3 + - + +
599A SER* 2.8 40.2 + - - +
600A PHE* 3.5 35.8 - - - +
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Residues in contact with THR 564 (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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59A TYR* 3.9 28.2 - - + -
152A PHE* 3.9 9.4 - - + -
154A SER* 4.3 22.2 - - - -
560A TYR* 2.5 52.5 + - + +
561A MET* 3.7 5.4 - - - -
563A ARG* 1.3 76.4 - - - +
565A MET* 1.3 61.1 + - - +
567A GLU* 3.3 12.6 - - - +
568A SER* 3.3 17.2 + - - -
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Residues in contact with MET 565 (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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56A ILE* 5.4 3.4 - - + -
59A TYR* 3.4 39.5 - - + -
510A VAL* 3.9 13.6 - - + +
513A ALA* 3.8 27.1 - - + +
514A ILE* 3.6 38.8 - - + +
517A THR* 4.5 7.0 - - - +
561A MET* 2.9 45.3 + - + +
562A VAL* 3.8 3.8 - - - +
564A THR* 1.3 73.0 - - - +
566A LEU* 1.3 64.5 + - - +
567A GLU 3.1 1.6 - - - -
568A SER* 2.5 25.6 + - - -
569A LEU* 3.4 9.9 + - - +
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Residues in contact with LEU 566 (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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487A PHE* 3.7 25.8 - - + -
492A LEU* 4.7 3.6 - - + -
514A ILE* 3.6 20.4 - - + -
562A VAL* 2.9 28.3 + - + +
563A ARG* 3.7 6.7 - - - +
565A MET* 1.3 75.2 - - - +
567A GLU* 1.3 62.8 + - - +
569A LEU* 3.1 26.3 + - + +
570A ILE* 3.4 14.7 + - - +
592A ILE* 3.7 29.9 - - + +
595A PHE* 3.5 37.7 - - + -
596A HIS* 4.7 9.0 - - + -
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Residues in contact with GLU 567 (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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152A PHE* 3.8 9.8 - - + -
153A VAL 3.8 4.2 - - - +
154A SER* 3.1 15.2 - - - -
155A GLU* 2.6 56.4 + - + +
156A ALA 5.0 0.9 + - - -
563A ARG* 2.9 20.5 + - - +
564A THR* 3.3 10.3 - - - +
565A MET 3.1 0.2 - - - -
566A LEU* 1.3 78.5 - - - +
568A SER* 1.3 59.6 + - - +
570A ILE* 3.6 12.3 + - + +
571A ALA* 3.2 22.5 + - + +
596A HIS* 3.5 24.5 + - + +
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Residues in contact with SER 568 (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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58A ARG* 5.2 2.9 - - - -
59A TYR* 3.4 22.6 + - - -
152A PHE* 3.9 31.8 - - - -
510A VAL* 4.5 4.5 - - - +
564A THR 3.3 3.4 + - - -
565A MET 2.5 21.9 + - - -
567A GLU* 1.3 78.0 - - - +
569A LEU* 1.3 66.3 + - - +
571A ALA* 3.7 12.4 + - - +
580A LEU* 3.6 23.4 + - - +
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Residues in contact with LEU 569 (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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507A ILE* 4.4 18.6 - - + -
510A VAL* 3.7 31.4 - - + -
511A LEU* 3.8 27.6 - - + -
514A ILE* 4.7 0.4 - - + -
565A MET 3.5 12.1 - - - +
566A LEU* 3.1 18.5 + - + +
568A SER* 1.3 78.4 - - - +
570A ILE* 1.3 59.4 + - - +
571A ALA 3.2 1.1 + - - -
580A LEU* 3.7 21.7 - - + -
581A ARG* 3.2 30.7 + - - -
584A LEU* 3.8 16.2 - - + +
592A ILE* 4.1 18.2 - - + -
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Residues in contact with ILE 570 (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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566A LEU 3.7 7.6 - - - +
567A GLU* 3.7 15.0 - - + +
569A LEU* 1.3 77.0 - - - +
571A ALA* 1.3 60.5 + - - +
581A ARG* 2.9 39.8 + - - +
584A LEU* 5.2 0.2 - - + -
589A ILE* 4.3 12.6 - - + -
592A ILE* 3.6 33.2 - - + -
593A GLU* 3.8 34.8 - - + +
596A HIS* 4.5 23.1 - - + +
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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