Contacts of the strand formed by residues 654 - 662 (chain A) in PDB entry 4NEN
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 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A LEU* 4.0 17.4 - - - +
639A ILE* 4.7 7.0 - - - -
652A LEU 4.5 3.4 - - - -
653A GLN* 1.3 75.9 - - - +
655A SER* 1.3 60.0 + - - +
656A VAL* 3.7 1.4 + - - +
686A VAL* 3.6 1.5 - - - +
687A LEU* 2.5 49.2 + - - +
719A LEU* 3.2 40.2 - - - +
721A GLY* 3.9 4.6 - - - -
722A LYS* 4.0 6.3 - - - +
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Residues in contact with SER 655 (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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654A SER* 1.3 72.0 + - - +
656A VAL* 1.3 64.0 + - - +
657A THR* 5.3 2.6 + - - -
684A VAL* 5.7 4.0 - - - +
685A ARG 4.0 7.4 + - - -
686A VAL* 4.3 9.0 - - - +
718A THR 4.0 0.2 - - - +
719A LEU* 3.5 2.6 - - - +
720A VAL* 2.8 51.3 + - - +
722A LYS* 3.9 21.0 - - - +
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Residues in contact with VAL 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A LEU* 4.8 3.8 - - + -
639A ILE* 4.9 1.3 - - + -
654A SER* 4.0 6.3 - - - +
655A SER* 1.3 82.6 + - - +
657A THR* 1.3 63.5 + - - +
658A LEU* 3.6 23.7 + - + +
683A ARG 3.6 1.6 - - - +
684A VAL* 3.5 4.4 - - - +
685A ARG* 3.2 29.5 + - + +
687A LEU* 3.7 30.5 - - + -
717A PHE* 3.7 23.3 - - + -
718A THR 3.4 9.9 - - - +
719A LEU* 3.7 25.6 - - + -
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Residues in contact with THR 657 (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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655A SER* 5.3 2.4 + - - -
656A VAL* 1.3 71.5 - - - +
658A LEU* 1.3 68.5 + - - +
659A ASP* 3.9 10.0 + - - +
682A SER* 5.7 3.4 - - - -
683A ARG 3.3 9.0 - - - +
684A VAL* 3.4 20.8 - - + +
717A PHE* 3.1 24.0 - - - -
718A THR* 3.0 26.8 + - - +
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Residues in contact with LEU 658 (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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635A ILE* 5.0 6.1 - - + -
637A LEU* 3.9 25.8 - - + -
656A VAL* 3.6 31.4 - - + +
657A THR* 1.3 73.7 - - - +
659A ASP* 1.3 70.5 + - - +
660A LEU* 5.4 7.2 - - + -
681A LEU* 6.4 0.4 - - + -
682A SER* 3.2 5.1 - - - -
683A ARG* 2.6 50.9 + - + +
685A ARG* 5.7 7.0 - - + +
687A LEU* 5.5 1.3 - - + -
694A GLU* 5.9 1.3 - - - +
696A PHE* 5.1 13.7 - - + -
715A LEU* 4.3 23.8 - - + -
716A ASN 3.6 4.7 - - - +
717A PHE* 4.5 7.2 - - + -
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Residues in contact with ASP 659 (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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657A THR* 3.9 10.8 + - - +
658A LEU* 1.3 82.8 - - - +
660A LEU* 1.3 74.2 + - - +
681A LEU 3.5 3.6 - - - +
682A SER* 3.3 16.3 + - - -
714A ARG* 6.1 1.6 - - - +
715A LEU* 3.8 2.1 - - - +
716A ASN* 3.0 51.2 + - - +
717A PHE* 6.4 0.2 - - - -
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Residues in contact with LEU 660 (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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635A ILE* 4.2 13.0 - - + -
658A LEU* 5.4 8.3 - - + -
659A ASP* 1.3 85.3 - - - +
661A ALA* 1.3 61.9 + - - +
673A PHE* 3.5 29.4 - - + -
679A ARG 4.2 1.3 - - - -
680A SER* 3.5 24.4 + - - -
681A LEU* 3.0 36.6 + - + +
696A PHE* 4.4 24.5 - - + -
713A LEU* 3.9 13.0 - - + -
714A ARG* 3.5 13.0 - - - +
715A LEU* 4.1 19.1 - - + -
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Residues in contact with ALA 661 (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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660A LEU* 1.3 76.8 - - - +
662A LEU* 1.3 64.1 + - - +
663A ASP 3.9 1.0 + - - -
664A PRO* 4.0 14.9 - - + +
679A ARG* 3.6 6.5 - - - +
680A SER* 5.5 1.3 - - - +
712A THR 3.7 0.2 - - - +
713A LEU* 3.3 8.4 - - - +
714A ARG* 2.8 72.0 + - + +
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Residues in contact with LEU 662 (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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608A PHE* 6.2 0.2 - - + -
661A ALA* 1.3 70.8 - - - +
663A ASP* 1.3 73.8 + - - +
669A PRO* 3.7 3.1 - - - +
671A ALA* 3.4 46.4 - - + +
672A THR* 3.6 15.9 - - - +
673A PHE* 3.6 27.6 - - + +
679A ARG* 3.3 35.4 + - + +
698A LEU* 3.7 21.1 - - + -
711A ILE* 4.9 2.9 - - + -
712A THR 3.6 8.5 - - - +
713A LEU* 3.6 26.5 - - + -
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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