Contacts of the strand formed by residues 653 - 662 (chain D) in PDB entry 1LQF
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 653 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A ILE 4.3 2.9 + - - -
782A MET 5.5 0.5 - - - -
648D ASP 5.6 0.2 - - - -
650D LYS* 2.9 52.8 + - + +
651D SER 3.5 0.6 - - - -
652D TYR* 1.3 96.0 - + + +
654D THR* 1.3 65.8 + - - +
655D VAL* 4.0 24.9 - - + -
674D PHE* 6.1 0.2 - + - -
675D HIS 3.1 15.0 - - - +
676D TYR* 3.8 4.5 - + + -
677D THR* 3.6 4.0 + - - -
690D SER 4.5 3.1 - - - -
693D ASN* 2.7 29.1 + - - -
694D PHE* 3.5 43.7 - + + -
697D LYS* 3.2 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 654 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D GLU* 3.9 12.1 - - + -
648D ASP 3.4 7.9 - - - +
649D ILE* 3.5 35.4 - - + +
653D TYR* 1.3 78.7 + - - +
655D VAL* 1.3 66.9 + - - +
656D ARG* 3.7 36.0 + - + +
673D HIS 3.3 3.1 - - - +
674D PHE* 3.8 0.5 - - - -
675D HIS* 2.8 39.0 + - - +
677D THR* 4.2 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646D SER* 4.1 3.2 + - - +
647D GLU* 3.2 2.1 + - - -
648D ASP* 2.7 46.8 + - + +
650D LYS* 6.4 0.2 - - + -
653D TYR* 4.0 26.0 - - + -
654D THR* 1.3 76.1 - - - +
656D ARG* 1.3 69.9 + - - +
672D LEU* 5.3 6.1 - - + -
673D HIS 3.4 8.7 - - - +
674D PHE* 4.0 33.2 - - + -
697D LYS* 6.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625D TRP* 3.3 43.1 - - - +
626D PRO 5.1 0.2 + - - -
644D LEU* 4.1 11.7 - - + -
646D SER* 3.6 9.2 - - - +
647D GLU* 3.5 36.6 + - + -
649D ILE* 5.4 1.8 - - - +
654D THR* 3.7 19.2 + - + +
655D VAL* 1.3 81.1 - - - +
657D GLN* 1.3 62.2 + - - +
658D LEU* 4.8 2.7 - - + -
671D ILE 4.0 0.2 - - - +
672D LEU* 3.7 6.5 - - - +
673D HIS* 2.9 58.7 + - + +
675D HIS* 3.6 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C ARG* 3.8 13.5 - - - +
644D LEU* 3.7 1.0 - - - +
645D ILE* 2.8 60.1 + - + +
646D SER* 3.0 33.3 + - - +
656D ARG* 1.3 74.4 - - - +
658D LEU* 1.3 65.4 + - - +
670D GLU* 2.5 36.6 + - + +
671D ILE 4.0 2.2 - - - -
672D LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D TRP* 4.1 26.5 - - + -
625D TRP* 4.5 9.2 - - + -
626D PRO* 4.1 20.6 - - + -
642D LEU* 4.0 15.0 - - + -
643D THR 3.5 10.3 - - - +
644D LEU* 3.9 26.5 - - + -
645D ILE* 4.0 3.4 - - - -
656D ARG* 4.8 2.0 - - + -
657D GLN* 1.3 78.0 - - - +
659D GLU* 1.3 60.5 + - - +
660D LEU 4.0 0.7 - - - -
670D GLU* 3.4 9.7 - - - +
671D ILE* 3.0 42.5 + - + +
673D HIS* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C ARG* 3.8 26.9 + - - -
641D LYS 3.6 1.6 - - - +
642D LEU* 3.6 5.0 - - - -
643D THR* 3.0 45.4 + - - +
645D ILE* 3.7 22.4 - - + +
658D LEU* 1.3 73.3 - - - +
660D LEU* 1.3 58.2 + - - +
661D GLU* 4.0 0.7 + - - +
668D THR* 2.8 41.6 + - + -
669D ARG* 3.5 15.0 + - - +
670D GLU* 4.2 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D TRP* 4.1 29.2 - - + +
599D VAL* 4.1 26.0 - - + -
600D TRP* 3.6 31.3 - - + +
635D PHE* 5.8 0.2 - - + -
640D LEU* 4.2 22.4 - - + -
641D LYS 3.5 15.0 - - - +
642D LEU* 4.2 17.3 - - + -
658D LEU 4.0 0.8 - - - -
659D GLU* 1.3 72.1 - - - +
661D GLU* 1.3 59.8 + - - +
668D THR* 3.2 3.3 - - - -
669D ARG* 2.9 40.9 + - + +
671D ILE* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 661 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D TRP* 4.4 0.2 - - - -
640D LEU* 3.4 8.7 - - - +
641D LYS* 2.9 62.8 + - + +
659D GLU* 4.0 1.1 + - + +
660D LEU* 1.3 73.5 - - - +
662D ASN* 1.3 71.4 + - - +
663D LEU* 3.3 23.2 + - - +
666D GLN* 3.9 27.3 - - - +
667D GLU 3.4 5.6 - - - +
668D THR* 3.2 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 662 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D TRP* 3.6 41.5 - - + +
639D ASN* 4.0 7.8 - - - +
640D LEU* 4.1 7.6 - - - -
661D GLU* 1.3 71.5 - - - +
663D LEU* 1.3 54.6 + - - +
664D THR* 2.8 37.3 + - - -
665D THR* 3.5 32.1 + - - +
666D GLN* 2.7 35.3 + - - -
667D GLU* 2.9 8.0 + - - +
----------------------------------------------------------
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