Contacts of the strand formed by residues 604 - 609 (chain D) in PDB entry 1V40
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 TYR 604 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596C GLN* 2.7 34.5 + - - +
602D PRO* 3.8 39.9 - - + +
603D ASN* 1.3 73.4 - - - +
605D LYS* 1.3 60.2 + - - +
606D LEU 4.2 0.2 - - - -
622D PHE* 3.9 12.3 - + + -
627D ILE* 3.8 22.9 - - + +
628D GLN 3.8 14.6 - - - -
629D TYR* 3.7 16.4 - - + -
630D GLU 2.9 13.1 + - - -
654D LEU* 4.0 12.8 - - + -
655D GLU 3.3 3.4 - - - -
656D VAL* 3.8 35.7 - - + -
670D TYR* 4.5 10.0 + + - -
671D LEU* 3.9 26.0 - - + +
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Residues in contact with LYS 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C GLN* 5.4 0.2 - - - +
604D TYR* 1.3 75.5 - - - +
606D LEU* 1.3 61.1 + - - +
607D THR* 3.9 6.8 + - - +
630D GLU* 3.5 44.7 + - + +
632D HIS* 3.8 33.1 + - + -
653D ILE* 3.8 0.9 - - - +
654D LEU* 3.5 4.9 - - - +
655D GLU* 2.9 64.2 + - + +
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Residues in contact with LEU 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D TYR 4.2 0.2 - - - -
605D LYS* 1.3 72.3 - - - +
607D THR* 1.3 63.0 + - - +
608D TYR* 5.0 1.8 - - + +
615D ALA* 4.3 8.7 - - + -
618D ILE* 4.1 29.8 - - + -
619D ARG* 3.7 33.4 - - + +
622D PHE* 4.9 0.4 - - + -
629D TYR* 3.9 17.2 - - + -
630D GLU 2.8 14.1 + - - +
631D ASP* 3.9 11.7 - - - +
632D HIS* 2.8 34.2 + - - +
652D PRO* 4.0 21.8 - - + -
653D ILE 3.5 16.8 - - - +
654D LEU* 3.9 10.9 - - + +
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Residues in contact with THR 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605D LYS* 3.9 9.9 + - - +
606D LEU* 1.3 74.3 - - - +
608D TYR* 1.3 65.5 + - - +
632D HIS* 3.4 20.6 - - + +
634D ILE* 4.0 26.2 - - + -
642D ILE* 4.8 10.5 - - + -
651D ILE* 3.7 16.1 - - + +
652D PRO* 3.2 25.5 - - - +
653D ILE* 3.0 35.2 + - + +
655D GLU* 4.4 5.4 + - - -
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Residues in contact with TYR 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D LEU* 4.2 2.0 + - + -
607D THR* 1.3 76.3 - - - +
609D PHE* 1.3 85.8 + + - +
611D MET* 3.6 27.4 - - + -
612D ARG 3.5 18.2 - - - -
613D GLY* 3.5 4.0 - - - -
614D ARG 2.8 22.2 + - - -
615D ALA* 3.5 25.6 - - + -
619D ARG* 3.9 7.0 - - - +
632D HIS 3.1 5.2 + - - -
633D ARG* 3.2 5.9 - - - -
634D ILE* 2.9 29.6 + - - +
651D ILE* 3.9 14.6 - - + -
652D PRO* 3.5 37.5 - - + -
3800D GSH 3.2 32.0 - - + -
3801D O16 4.6 4.3 - - - -
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Residues in contact with PHE 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D TYR* 1.3 104.3 - + - +
610D ASN* 1.3 62.2 + - - +
611D MET* 2.9 37.3 + - + -
619D ARG* 3.6 8.5 + - - -
633D ARG* 3.9 2.3 - - - +
634D ILE* 3.6 26.5 - - + +
636D GLN* 3.9 35.0 - - + -
639D TRP* 3.8 41.3 - + + -
651D ILE* 3.6 19.7 - - + -
3800D GSH 4.4 18.2 - - + -
3801D O16 4.3 15.9 - + - -
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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