Contacts of the strand formed by residues 553 - 562 (chain A) in PDB entry 1PD0
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 CYS 553 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 3.2 30.7 - - - -
552A PHE* 1.3 77.8 - - - +
554A MET* 1.3 65.6 + - - +
556A THR* 3.2 17.9 - - - +
587A THR* 2.9 26.3 - - - -
588A MET* 3.1 16.6 + - + -
590A ARG* 3.3 22.2 - - - -
617A LEU* 3.7 18.8 - - + -
618A SER 3.5 10.5 - - - +
619A LEU* 4.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO* 3.5 33.0 - - + +
303A PRO 3.5 25.4 - - - +
304A ALA* 4.0 7.2 - - - +
305A THR 4.9 1.6 - - - -
439A GLY 5.8 2.5 - - - +
440A GLY* 5.7 6.7 - - - +
494A GLN* 6.2 0.7 - - + -
552A PHE* 3.8 13.7 - - + -
553A CYS* 1.3 80.8 - - - +
555A GLU* 1.3 77.9 + - + +
556A THR* 2.9 9.3 + - - -
586A SER 3.2 12.3 - - - +
587A THR* 3.9 4.7 - - + +
618A SER* 3.0 27.5 + - - +
619A LEU 3.6 21.5 - - - +
620A ASN* 3.7 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ARG* 2.6 54.7 + - - +
301A PRO* 4.9 1.0 - - - +
302A PRO* 3.5 23.2 - - + +
494A GLN* 3.5 33.0 - - + +
554A MET* 1.3 73.7 - - + +
556A THR* 1.3 61.6 + - - +
557A VAL* 4.5 5.5 - - - +
585A PHE 4.1 0.2 - - - -
586A SER 3.0 11.7 + - - -
616A LEU* 3.9 2.1 - - - +
618A SER* 3.5 9.6 + - - +
624A ARG* 3.5 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLN* 5.1 1.2 - - - +
553A CYS* 3.2 19.6 - - - +
554A MET 3.2 3.9 + - - -
555A GLU* 1.3 74.9 - - - +
557A VAL* 1.3 76.7 + - - +
584A ALA* 3.8 0.7 - - - +
585A PHE* 2.8 43.3 + - + +
588A MET* 4.1 18.8 - - + -
615A VAL* 3.4 27.4 - - + -
616A LEU 3.2 11.2 - - - +
617A LEU* 3.0 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLN* 6.1 0.7 - - - +
555A GLU 4.5 6.1 - - - +
556A THR* 1.3 85.6 - - - +
558A MET* 1.3 60.6 + - - +
582A LEU* 4.2 29.8 - - + -
583A CYS 3.2 10.1 - - - +
584A ALA* 4.6 9.9 - - + -
585A PHE* 4.8 0.2 - - - -
614A ALA 3.8 0.7 - - - +
615A VAL* 3.5 3.3 - - - -
616A LEU* 3.0 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 4.4 7.4 - - + -
209A PRO* 3.8 26.2 - - - -
557A VAL* 1.3 76.7 - - - +
559A ARG* 1.3 66.2 + - - +
575A PHE* 5.8 0.2 - - + -
582A LEU* 3.7 2.4 - - - -
583A CYS* 2.8 41.9 + - + +
585A PHE* 3.9 31.9 - - + -
588A MET* 4.0 8.7 - - + -
594A TYR* 4.3 17.9 - - + -
596A PHE* 3.8 29.2 - - + -
613A VAL* 4.0 16.6 - - + -
614A ALA 3.3 11.7 - - - +
615A VAL* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A MET* 1.3 76.6 - - - +
560A ALA* 1.3 64.6 + - - +
561A ARG* 3.3 46.4 - - + +
581A ASP* 3.1 46.4 + - - +
582A LEU* 3.4 37.6 - - + +
596A PHE* 4.4 6.3 - - - -
612A GLN 3.9 0.5 - - - +
613A VAL* 3.3 4.3 - - - +
614A ALA* 2.8 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 5.0 0.2 - - + -
207A ILE* 4.9 0.7 - - + -
559A ARG* 1.3 77.4 + - - +
561A ARG* 1.3 62.2 + - - +
562A GLY 4.1 0.2 + - - -
568A MET* 3.0 31.8 - - + +
581A ASP* 4.6 9.3 + - - +
596A PHE* 3.6 29.9 - - + -
611A VAL* 4.7 6.1 - - + -
612A GLN 3.2 6.7 - - - +
613A VAL* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG* 3.3 26.0 - - - +
234A CYS* 3.3 21.2 + - + -
235A ARG* 3.7 12.2 - - - +
236A SER* 3.4 32.8 - - - +
237A TYR* 4.2 6.1 - - - -
255A PHE* 3.9 2.7 - - + -
559A ARG* 3.3 46.4 - - + +
560A ALA* 1.3 77.1 - - - +
562A GLY* 1.3 63.5 + - - +
568A MET* 5.2 0.9 - - - -
581A ASP* 6.1 0.2 - - - +
611A VAL* 3.5 4.5 - - - +
612A GLN* 2.7 43.9 + - + +
614A ALA* 4.0 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 3.8 9.7 - - - +
560A ALA 4.1 0.8 + - - -
561A ARG* 1.3 78.3 - - - +
563A SER* 1.3 67.8 + - - -
566A LEU* 4.2 22.8 + - - +
567A ARG* 5.9 0.6 - - - +
568A MET* 5.1 7.7 - - - +
610A TYR 3.4 8.1 - - - -
611A VAL* 4.5 4.0 - - - -
----------------------------------------------------------
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