Contacts of the strand formed by residues 623 - 631 (chain A) in PDB entry 3NKO
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 MET 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617A TYR* 3.5 11.2 - - - -
618A SER* 2.9 26.8 + - - -
621A PHE* 3.3 26.2 - - + +
622A LEU* 1.3 79.4 - - - +
624A PRO* 1.3 83.2 - - + +
625A LEU* 4.5 0.6 - - + +
660A GLN* 3.7 10.1 - - - +
697A MET 4.8 0.2 - - - -
698A VAL* 4.1 15.5 - - + -
699A PRO* 3.8 15.5 - - + -
732A PRO* 3.9 26.9 - - + -
734A PHE* 4.1 7.4 - - + -
757A ILE* 4.2 6.5 - - + -
758A PRO* 3.2 31.9 - - + +
760A PRO* 4.1 5.6 - - - -
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Residues in contact with PRO 624 (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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615A SER* 4.2 10.8 - - - -
616A GLY 3.3 9.4 - - - +
617A TYR* 3.8 6.7 - - + -
623A MET* 1.3 91.2 - - + +
625A LEU* 1.3 59.4 + - - +
626A TRP 3.6 12.3 - - - +
627A THR* 3.6 24.5 - - - +
676A LEU* 4.0 13.5 - - + -
695A THR 3.2 29.6 - - - +
696A ASN* 4.8 3.6 - - - +
697A MET 4.7 1.6 - - - +
698A VAL* 4.6 3.6 - - + -
732A PRO* 3.0 29.1 - - - +
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Residues in contact with LEU 625 (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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599A VAL* 4.1 24.7 - - + -
601A TYR* 3.5 27.8 - - + +
603A THR* 4.7 4.9 - - + -
605A TYR* 4.4 20.0 - - + -
616A GLY 2.8 13.7 + - - +
618A SER* 3.5 25.1 - - - +
621A PHE* 4.4 11.2 - - + -
623A MET* 4.5 0.9 - - + +
624A PRO* 1.3 74.9 - - - +
626A TRP* 1.3 61.5 + - + +
732A PRO* 4.0 10.6 - - + +
734A PHE* 6.3 1.1 - - + -
764A TYR* 2.8 31.2 + - - -
829A THR* 5.3 1.0 - - - +
831A LEU* 3.6 14.4 - - + +
1013A EDO 4.8 5.6 - - - -
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Residues in contact with TRP 626 (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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592A LEU* 4.0 9.2 - - + -
596A ARG* 4.4 5.6 - - + -
597A PRO* 3.6 43.4 + - + +
599A VAL* 5.2 1.6 - - - +
605A TYR* 4.6 9.2 - + - -
607A ILE* 3.8 13.7 - - + -
614A GLU* 3.7 28.5 - - + -
615A SER* 3.2 28.8 - - - -
616A GLY* 3.1 34.0 + - - -
624A PRO* 3.1 3.5 - - - +
625A LEU* 1.3 92.4 - - + +
627A THR* 1.3 65.9 + - - +
628A SER* 3.9 20.0 - - - -
729A ILE* 3.8 10.1 - - + -
730A SER 3.4 8.5 - - - -
764A TYR* 3.2 11.2 - - - +
831A LEU* 3.9 19.3 - - + +
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Residues in contact with THR 627 (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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613A PHE* 3.9 27.4 - - + -
614A GLU 3.4 4.0 - - - +
615A SER* 4.0 2.5 - - - -
624A PRO* 3.6 9.5 - - - +
626A TRP* 1.3 76.1 + - - +
628A SER* 1.3 62.2 + - - +
629A TYR* 4.2 8.8 - - + -
676A LEU* 3.2 31.7 - - + +
677A PHE* 3.9 25.1 - - + +
696A ASN* 4.3 2.6 + - - +
728A VAL 3.5 1.4 - - - +
729A ILE* 3.2 3.4 - - - -
730A SER* 2.8 36.8 + - - -
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Residues in contact with SER 628 (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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591A HIS* 2.6 29.9 + - - +
592A LEU* 3.6 26.4 - - - +
613A PHE* 3.5 0.9 - - - -
614A GLU* 2.7 34.7 + - - -
626A TRP* 3.9 12.1 - - - -
627A THR* 1.3 74.3 - - - +
629A TYR* 1.3 63.8 + - - +
727A ASN* 3.9 3.8 + - - -
728A VAL 3.2 5.6 + - - -
729A ILE* 3.7 17.8 - - - +
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Residues in contact with TYR 629 (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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591A HIS* 3.4 7.2 - - - -
612A ASP 3.2 21.8 - - - +
613A PHE* 3.7 3.4 - - + -
627A THR* 4.2 13.9 - - + -
628A SER* 1.3 81.4 + - - +
630A THR* 1.3 62.3 + - - +
631A ILE* 3.6 31.0 - - + -
676A LEU 4.0 14.8 + - - -
677A PHE* 3.5 24.9 - + - -
678A PRO* 3.7 12.2 - - + +
681A LEU* 4.3 3.8 - - + -
711A PHE* 5.0 0.2 - - - -
712A GLN* 3.7 18.7 + - - -
716A VAL* 4.0 11.9 - - + +
726A VAL 4.0 0.3 - - - +
727A ASN* 3.5 2.7 + - - -
728A VAL* 2.8 72.6 + - + +
730A SER* 4.7 3.1 + - - -
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Residues in contact with THR 630 (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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590A ARG* 3.1 45.9 + - - +
591A HIS* 2.8 24.4 + - - -
593A LEU* 3.7 17.9 - - + +
612A ASP 5.1 0.2 - - - +
629A TYR* 1.3 73.9 - - - +
631A ILE* 1.3 77.0 + - - +
632A SER* 4.1 1.3 - - - +
726A VAL 3.5 14.6 - - - +
727A ASN* 2.9 20.3 + - - -
777A ALA* 4.7 6.3 - - + -
778A ASP* 4.7 9.6 - - + -
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Residues in contact with ILE 631 (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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629A TYR* 3.6 28.5 - - + -
630A THR* 1.3 84.0 - - - +
632A SER* 1.3 65.7 + - - +
635A ALA* 3.7 16.2 - - + -
677A PHE* 4.7 3.6 - - + -
681A LEU* 3.8 43.1 - - + +
716A VAL* 4.1 14.4 - - + +
717A LYS* 5.0 4.0 - - + -
720A ALA* 3.6 20.1 - - + +
725A GLY* 3.0 4.9 - - - -
726A VAL* 2.8 43.5 + - + +
728A VAL* 5.2 0.2 - - + -
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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