Contacts of the strand formed by residues 570 - 575 (chain A) in PDB entry 2EIE
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 LYS 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A GLU* 5.9 5.3 - - - +
568A ILE* 4.5 1.2 - - - +
569A SER* 1.3 92.7 + - - +
571A ALA* 1.3 61.8 + - - +
592A LEU 5.8 0.9 - - - -
594A LEU* 3.9 7.3 - - - +
622A VAL* 3.6 2.6 - - - +
623A MET* 2.8 47.1 + - + +
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Residues in contact with ALA 571 (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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570A LYS* 1.3 78.9 - - - +
572A SER* 1.3 62.6 + - - +
589A ARG* 5.5 0.7 + - - -
591A PRO* 4.0 2.3 - - - +
592A LEU* 3.0 38.2 + - + +
594A LEU* 3.8 30.6 - - + +
620A LEU* 4.7 2.0 - - + -
621A PHE 3.2 15.0 - - - +
622A VAL* 4.0 12.1 - - + -
623A MET* 4.1 4.0 - - - -
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Residues in contact with SER 572 (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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448A PRO* 2.9 35.1 + - - +
571A ALA* 1.3 77.1 - - - +
573A LEU* 1.3 59.5 + - - +
574A ILE* 4.1 4.8 - - - +
589A ARG* 3.8 18.8 + - - -
590A ILE 3.4 11.7 - - - -
591A PRO* 4.4 1.8 - - - -
592A LEU* 4.0 7.0 - - - -
619A MET 3.5 1.6 - - - +
620A LEU* 3.6 4.5 - - - +
621A PHE* 2.9 37.6 + - - +
623A MET* 3.9 4.3 - - - +
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Residues in contact with LEU 573 (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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572A SER* 1.3 72.1 - - - +
574A ILE* 1.3 61.2 + - - +
589A ARG* 3.4 3.6 - - - +
590A ILE* 2.8 44.9 + - + +
592A LEU* 3.9 25.6 - - + -
604A PHE* 4.6 6.7 - - + -
606A VAL* 4.3 28.0 - - + -
618A TRP* 3.6 30.7 - - + -
619A MET 3.3 4.0 - - - +
620A LEU* 3.9 35.4 - - + +
635A ILE* 4.7 11.2 - - + -
637A VAL* 5.0 5.8 - - + -
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Residues in contact with ILE 574 (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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446A VAL* 4.0 15.5 - - + +
447A LEU 3.6 9.4 - - - +
448A PRO* 3.5 36.8 - - + -
501A LEU* 3.7 29.8 - - + -
572A SER* 4.3 5.2 - - - +
573A LEU* 1.3 77.2 - - - +
575A ARG* 1.3 71.8 + - - +
576A TYR 3.5 0.5 + - - -
587A GLN* 5.3 2.7 - - + +
588A ARG 3.4 9.9 - - - +
589A ARG* 4.2 13.2 - - + -
618A TRP* 3.7 3.1 - - - -
619A MET* 2.7 45.5 + - + +
621A PHE* 4.0 12.6 - - + -
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Residues in contact with ARG 575 (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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233A MET* 2.8 33.5 + - - +
234A ASP 4.2 1.6 + - - -
277A THR* 3.6 8.9 - - - +
574A ILE* 1.3 79.7 - - - +
576A TYR* 1.3 70.5 + - - +
577A GLY 3.5 1.7 + - - -
586A ASP* 2.8 54.8 + - - +
587A GLN* 3.5 12.8 - - - +
588A ARG* 3.0 20.7 + - + +
614A LEU* 3.4 33.8 + - - +
615A PRO 2.8 21.6 + - - -
616A GLY* 4.4 3.9 - - - -
617A TYR 3.5 13.7 - - - +
618A TRP* 3.3 35.1 - - + +
619A MET* 4.4 1.2 - - - +
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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