Contacts of the strand formed by residues 650 - 656 (chain D) in PDB entry 1M7X
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 GLU 650 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D LEU* 5.8 0.2 - - - +
642D VAL* 3.4 23.8 - - + +
643D ARG 3.2 7.4 - - - +
644D ARG* 2.7 40.5 + - + +
648D GLY 3.5 10.9 - - - +
649D ASN* 1.3 74.9 - - - +
651D ILE* 1.3 68.0 + - - +
670D ASN* 3.3 33.8 + - - +
671D GLN* 3.2 29.5 + - - +
675D TRP* 3.3 21.5 - - + -
724D VAL* 5.4 0.5 - - - +
725D ARG* 4.6 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 651 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D HIS* 5.1 10.8 - - + +
615D ALA* 3.7 18.6 - - + -
616D MET* 3.1 29.2 - - - -
642D VAL* 3.1 15.1 - - - +
643D ARG* 3.0 18.4 + - + +
649D ASN* 5.4 2.2 - - + -
650D GLU* 1.3 79.9 - - - +
652D ILE* 1.3 66.1 + - - +
653D VAL* 3.3 28.2 - - + +
675D TRP* 3.9 0.2 - - - -
678D ILE* 4.8 6.3 - - + -
722D TRP* 4.0 15.0 - - + -
723D LEU 3.1 13.9 - - - +
724D VAL* 4.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 652 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D LEU* 4.1 6.3 - - + -
640D ILE* 3.8 24.9 - - + -
641D PHE 3.7 3.1 - - - -
642D VAL* 3.9 10.5 - - + -
651D ILE* 1.3 73.6 - - - +
653D VAL* 1.3 63.6 + - - +
654D ALA* 4.8 1.6 - - + +
667D PHE* 3.8 12.6 - - + -
669D ILE* 3.4 33.7 - - + -
675D TRP* 3.5 26.9 - - + -
711D LEU* 3.5 20.6 - - + -
722D TRP* 3.3 4.3 - - - -
723D LEU* 2.7 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 653 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D GLY 4.8 0.7 - - - +
556D TRP* 5.3 2.5 - - + -
559D ALA* 3.7 33.4 - - + -
616D MET* 4.2 3.6 - - + -
639D LEU 3.9 1.0 - - - +
640D ILE* 3.2 3.5 - - - +
641D PHE* 2.7 68.8 + - + +
643D ARG* 4.7 1.3 - - + -
651D ILE* 3.3 27.4 - - + +
652D ILE* 1.3 71.8 - - - +
654D ALA* 1.3 64.7 + - - +
655D SER* 4.8 3.6 - - - +
720D THR* 4.5 8.7 - - - +
721D ILE 3.5 2.9 - - - +
722D TRP* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 654 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D LEU 3.5 3.8 - - - -
640D ILE* 3.5 29.6 - - + -
652D ILE* 4.1 5.7 - - + -
653D VAL* 1.3 73.8 - - - +
655D SER* 1.3 62.0 + - - +
656D ASN 4.3 0.2 + - - -
667D PHE* 5.5 2.0 - - + -
713D LEU* 5.5 0.7 - - + -
715D LEU* 4.0 21.4 - - + +
719D ALA 4.5 0.2 - - - +
720D THR* 3.5 1.3 - - - -
721D ILE* 2.9 46.6 + - + +
723D LEU* 5.1 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D TRP* 3.3 27.5 - - - +
637D SER 3.9 0.5 - - - +
638D VAL* 3.3 8.7 - - - +
639D LEU* 2.9 32.8 + - - +
653D VAL* 4.8 1.8 - - - +
654D ALA* 1.3 75.2 - - - +
656D ASN* 1.3 62.0 + - - +
657D PHE* 3.4 28.0 - - - -
715D LEU* 5.5 0.9 - - - -
719D ALA 3.7 5.8 - - - -
720D THR* 2.9 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636D ARG 3.8 12.1 + - - -
637D SER 4.0 0.9 - - - -
638D VAL* 3.8 11.6 - - + +
654D ALA 4.3 0.2 + - - -
655D SER* 1.3 71.9 - - - +
657D PHE* 1.3 65.0 + - - +
658D THR* 3.4 25.4 + - - +
660D VAL 2.7 25.0 + - - +
662D ARG* 3.8 6.7 - - - +
715D LEU* 3.5 18.6 - - + +
716D PRO* 3.3 26.0 - - + +
718D LEU* 3.3 6.8 - - - -
719D ALA 3.0 28.7 + - - +
----------------------------------------------------------
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