Contacts of the strand formed by residues 617 - 623 (chain A) in PDB entry 4N41
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 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573A VAL* 4.0 18.2 - - + -
574A ARG 3.7 10.1 - - - +
575A LYS* 4.2 2.0 - - - -
602A LEU* 3.3 7.0 - - - +
603A LEU* 2.8 39.6 + - + +
605A THR* 4.0 15.0 - - + +
615A ARG 3.5 0.4 + - - -
616A PRO* 1.3 73.8 - - - +
618A LYS* 1.3 59.8 + - - +
619A LEU* 3.5 17.6 - - + +
635A ILE* 5.5 0.7 - - + -
651A ARG* 3.4 66.6 - - + +
652A LEU* 4.1 16.8 - - + -
653A PRO* 4.5 7.6 - - + -
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Residues in contact with LYS 618 (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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573A VAL* 3.8 0.3 - - - -
574A ARG* 2.9 65.2 + - + +
577A GLY 3.8 19.3 + - - +
578A GLY* 4.0 17.2 - - - +
596A LEU* 5.5 7.0 - - + -
597A GLU* 4.5 16.3 + - - -
600A THR* 5.0 6.5 - - - -
601A PHE 3.7 4.7 - - - +
602A LEU* 4.2 11.9 - - + -
616A PRO 3.7 1.2 + - - -
617A LEU* 1.3 73.7 - - - +
619A LEU* 1.3 65.1 + - - +
620A VAL* 4.9 9.0 - - + -
3D A 5.5 0.2 + - - -
4D C 4.1 18.7 + - - +
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Residues in contact with LEU 619 (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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571A VAL* 4.0 6.7 - - + -
572A SER 3.1 9.9 - - - +
573A VAL* 4.0 14.4 - - + -
599A LYS 4.0 0.2 - - - +
600A THR* 3.3 5.0 - - - -
601A PHE* 2.9 63.2 + - + +
603A LEU* 3.6 18.2 - - + -
617A LEU* 3.5 32.1 - - + +
618A LYS* 1.3 80.0 - - - +
620A VAL* 1.3 66.1 + - - +
621A HIS 4.2 0.2 - - - -
635A ILE* 3.6 40.8 - - + -
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Residues in contact with VAL 620 (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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571A VAL* 3.4 4.9 - - - -
572A SER* 2.9 40.8 + - - -
574A ARG* 4.0 29.8 - - - +
599A LYS* 3.5 11.2 - - + +
600A THR* 3.8 21.1 - - + -
618A LYS* 4.9 7.4 - - - -
619A LEU* 1.3 79.6 - - - +
621A HIS* 1.3 66.9 + - - +
622A GLU* 3.3 22.0 + - + +
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Residues in contact with HIS 621 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A ASP* 2.8 22.8 + - + -
570A LEU 3.6 9.2 - - - -
571A VAL* 4.3 6.2 - - + +
599A LYS* 2.8 48.9 + - + +
601A PHE* 5.1 1.9 - - + -
619A LEU 4.2 0.2 - - - -
620A VAL* 1.3 71.7 - - - +
622A GLU* 1.3 59.1 + - - +
623A ALA 3.0 21.3 + - - -
624A GLY 3.4 19.7 + - - -
625A ASP* 4.3 1.1 - - - -
626A THR 3.1 27.9 + - - -
628A LEU* 3.5 26.0 - - + +
631A LEU* 3.6 19.1 - - + +
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Residues in contact with GLU 622 (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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545A ARG* 2.7 36.4 + - - -
551A GLN* 3.3 40.9 + - - +
570A LEU* 2.9 36.0 + - + +
572A SER* 3.6 14.7 - - - -
574A ARG* 4.6 7.6 + - - -
599A LYS* 5.5 5.3 - - - +
620A VAL* 3.6 23.1 - - + +
621A HIS* 1.3 74.8 - - - +
623A ALA* 1.3 62.9 + - - +
75B LEU* 5.8 2.3 - - - +
76B GLU* 4.9 0.5 - - - +
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Residues in contact with ALA 623 (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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551A GLN* 5.2 1.6 - - - +
558A LEU* 3.9 27.4 - - + -
568A TYR* 4.2 9.9 - - + -
569A ASP* 3.2 2.1 - - - -
570A LEU* 2.9 33.6 + - + -
621A HIS* 3.0 13.5 + - - -
622A GLU* 1.3 80.3 - - + +
624A GLY* 1.3 62.2 + - - +
76B GLU* 3.6 12.1 - - - +
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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