Contacts of the strand formed by residues 615 - 622 (chain C) in PDB entry 1UEX
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 615 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C LEU 3.3 6.4 + - - -
513C LEU* 3.5 8.3 - - - +
514C ASP* 3.0 27.2 + - - +
614C ALA* 1.3 75.1 - - - +
616C ARG* 1.3 63.8 + - - +
617C ILE* 4.9 4.0 - - - -
645C LYS 5.6 0.2 - - - -
647C ILE* 5.0 6.0 - - - +
697C LEU 2.6 30.0 + - - -
698C ALA* 3.9 8.7 - - - -
699C PRO* 3.3 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 616 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C ASP* 2.7 36.6 + - - +
552C ARG* 4.8 0.6 - - - +
606C PHE* 3.3 32.7 - - + -
608C LYS 5.0 0.4 + - - -
609C ILE* 3.0 45.1 - - - +
610C ASP* 3.9 2.4 + - - +
611C ARG* 3.1 37.4 + - - +
614C ALA* 3.9 8.9 + - - +
615C SER* 1.3 76.4 + - - +
617C ILE* 1.3 57.3 + - - +
644C LYS 4.5 9.9 - - - -
645C LYS* 3.8 9.9 + - - +
646C VAL* 3.6 26.5 - - + -
647C ILE* 2.6 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C LEU* 3.5 20.9 - - + -
514C ASP 2.9 10.4 + - - +
515C LEU* 3.4 19.9 - - + -
516C VAL* 2.9 27.5 + - - +
606C PHE* 4.7 0.6 - - - -
615C SER* 4.9 1.8 - - - -
616C ARG* 1.3 80.8 - - - +
618C ALA* 1.3 66.1 + - - +
619C LEU 4.4 0.4 - - - +
646C VAL* 4.7 2.5 - - - -
647C ILE* 3.2 16.6 - - + +
649C ILE* 3.7 27.1 - - + -
694C LEU* 3.5 35.9 - - + +
697C LEU* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C VAL* 3.8 7.4 - - + -
518C LEU* 4.5 17.3 - - + -
598C LEU* 5.1 3.1 - - + -
601C THR* 4.5 13.0 - - + -
617C ILE* 1.3 74.4 - - - +
619C LEU* 1.3 58.0 + - - +
620C LEU 3.1 5.6 + - - -
641C LEU* 5.7 0.2 - - + -
646C VAL* 4.4 12.3 - - + -
647C ILE 2.7 14.4 + - - +
648C VAL* 3.5 15.9 - - + +
649C ILE 2.8 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C LEU* 4.0 10.2 - - + +
516C VAL 2.9 14.1 + - - +
517C PHE* 3.4 35.0 - - + -
518C LEU* 3.2 25.0 + - - +
536C PHE* 3.9 21.3 - - + -
540C MET* 4.2 9.9 - - + -
617C ILE 3.9 2.0 - - - -
618C ALA* 1.3 70.0 - - - +
620C LEU* 1.3 57.1 + - - +
621C LEU* 3.2 13.8 + - + +
649C ILE* 3.7 27.8 - - + -
651C VAL* 4.0 13.2 - - + -
690C ILE* 4.3 6.5 - - + -
694C LEU* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU* 4.0 29.8 - - + -
558C TYR* 3.8 22.0 - - + +
594C THR* 4.4 9.0 - - + -
597C VAL* 4.1 9.9 - - + -
598C LEU* 4.1 18.4 - - + -
618C ALA 3.1 6.3 + - - +
619C LEU* 1.3 67.3 - - - +
621C LEU* 1.3 57.5 + - - +
622C MET* 3.0 30.2 + - + +
634C PHE* 5.5 0.9 - - + -
648C VAL* 4.5 5.8 - - + -
649C ILE 3.1 14.1 + - - +
650C PRO* 4.2 4.3 - - + -
651C VAL* 3.1 19.9 + - - -
665C ILE* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PHE* 4.2 22.7 - - + -
518C LEU 3.1 25.4 + - - +
519C LEU* 4.5 12.6 - - + -
520C ASP* 3.1 25.8 + - - +
533C LEU* 4.3 17.2 - - + +
536C PHE* 3.5 34.5 - - + -
537C VAL* 4.5 2.5 - - + -
558C TYR* 3.3 4.3 + - - -
619C LEU* 3.9 13.9 - - + +
620C LEU* 1.3 67.4 - - - +
622C MET* 1.3 58.7 + - - +
651C VAL* 3.7 30.5 - - + -
653C ILE* 4.3 7.2 - - + -
683C LEU* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C ASP* 4.1 1.3 - - - +
558C TYR* 3.4 18.2 - - - +
594C THR* 4.4 12.8 - - + -
620C LEU* 3.3 29.6 - - + +
621C LEU* 1.3 72.1 - - - +
623C ALA* 1.3 60.9 + - - +
624C SER 3.7 6.3 - - - +
650C PRO* 4.9 4.0 - - - -
651C VAL 2.9 20.6 + - - +
652C GLY* 3.5 2.0 - - - -
653C ILE* 2.9 26.3 + - - +
657C ALA* 3.8 4.5 - - + +
658C ASN* 3.2 47.1 - - + +
661C GLN* 4.9 3.8 - - + -
662C ILE* 3.4 28.7 - - + +
665C ILE* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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