Contacts of the strand formed by residues 3219 - 3233 (chain D) in PDB entry 3CMT
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 ALA3219 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3061D ILE* 3.3 14.2 - - - +
3063D GLU* 4.3 10.8 - - + +
3215D LEU* 2.9 21.5 + - + +
3216D LYS 4.2 0.4 - - - +
3217D PHE 3.3 1.1 - - - +
3218D TYR* 1.3 76.8 - - - +
3220D SER* 1.3 59.9 + - - +
3221D VAL 3.8 8.3 - - - +
3222D ARG* 3.7 28.9 - - + -
3248D LYS* 2.9 28.2 + - - -
3250D LYS* 4.1 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2098D ALA* 4.7 2.6 - - - +
3057D PRO* 4.4 8.7 - - - -
3060D ARG* 3.0 53.1 + - - +
3061D ILE 2.7 11.9 + - - -
3218D TYR 4.1 5.7 + - - -
3219D ALA* 1.3 73.4 - - - +
3221D VAL* 1.3 64.1 + - - +
3248D LYS* 4.5 2.2 - - - +
3249D ASN* 3.5 2.3 + - - -
3250D LYS* 2.8 44.1 + - - +
3251D ILE* 4.5 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3051D LEU* 3.6 21.1 - - + -
3056D LEU* 4.1 8.5 - - + -
3057D PRO* 4.1 25.4 - - + -
3061D ILE 3.8 2.0 + - - -
3062D VAL* 3.4 15.9 - - + +
3063D GLU 3.0 23.4 + - - -
3219D ALA* 3.8 1.2 - - - +
3220D SER* 1.3 86.0 - - - +
3222D ARG* 1.3 68.1 + - - +
3223D LEU* 3.5 26.9 - - + -
3246D VAL* 4.7 0.9 - - + -
3248D LYS 3.2 9.4 - - - +
3249D ASN* 3.7 17.0 - - - +
3251D ILE* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2068D GLU* 4.5 8.1 + - - -
3063D GLU* 2.5 50.3 + - + +
3065D TYR* 3.7 30.1 + - + -
3209D THR* 4.5 7.7 + - - +
3216D LYS* 4.0 45.0 + - - +
3219D ALA* 3.7 19.3 - - + -
3221D VAL* 1.3 78.8 - - - +
3223D LEU* 1.3 66.6 + - - +
3246D VAL* 3.7 0.5 - - - -
3247D VAL* 2.8 41.8 + - + +
3248D LYS* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3047D LEU* 4.5 17.0 - - + -
3051D LEU* 4.3 4.0 - - + -
3056D LEU* 4.2 22.2 - - + -
3062D VAL* 4.6 2.0 - - + -
3063D GLU 2.7 12.0 + - - +
3064D ILE* 3.4 30.6 - - + +
3065D TYR* 2.9 35.0 + - - +
3075D LEU* 4.9 4.9 - - + -
3221D VAL* 3.5 20.2 - - + -
3222D ARG* 1.3 80.9 - - - +
3224D ASP* 1.3 59.1 + - - +
3225D ILE 3.8 0.4 + - - -
3244D VAL* 3.6 20.0 - - + -
3245D LYS 3.5 2.0 - - - +
3246D VAL* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3065D TYR* 3.4 30.4 + - + +
3207D GLU* 5.0 0.5 - - - +
3222D ARG 4.2 0.6 + - - -
3223D LEU* 1.3 70.7 - - - +
3225D ILE* 1.3 61.4 + - - +
3226D ARG* 2.7 39.8 + - - +
3243D ARG 3.7 1.7 - - - +
3244D VAL* 3.4 2.7 - - - -
3245D LYS* 2.8 48.3 + - + +
3247D VAL* 3.6 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3064D ILE* 3.8 12.8 - - + -
3065D TYR 2.9 18.7 + - - +
3066D GLY* 3.4 2.3 - - - -
3067D PRO* 3.4 14.7 - - - +
3070D SER* 3.6 26.3 - - - +
3071D GLY* 3.8 18.8 - - - +
3072D LYS* 3.6 27.4 - - + +
3075D LEU* 4.0 15.9 - - + -
3223D LEU 3.8 0.4 - - - -
3224D ASP* 1.3 73.1 - - - +
3226D ARG* 1.3 73.4 + - - +
3242D THR* 3.7 21.3 - - + -
3243D ARG 3.5 2.7 - - - -
3244D VAL* 3.8 19.7 - - + +
3260D PHE* 4.6 1.3 - - + -
3262D ILE* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3065D TYR* 4.6 1.8 - - - -
3067D PRO* 3.4 25.1 - - + +
3070D SER* 4.2 8.7 - - - -
3195D ILE* 3.2 19.3 - - - +
3207D GLU* 2.7 40.0 + - - -
3224D ASP* 2.7 35.1 + - - +
3225D ILE* 1.3 79.4 - - - +
3227D ARG* 1.3 65.0 + - - +
3228D ILE* 3.6 9.1 + - + +
3242D THR* 3.6 3.6 - - - +
3243D ARG* 2.9 38.8 + - + +
3245D LYS* 5.8 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3067D PRO* 5.5 1.6 - - - +
3068D GLU 6.0 0.2 - - - +
3069D SER* 4.6 17.0 - - - +
3070D SER* 4.2 12.2 - - - +
3226D ARG* 1.3 74.5 - - - +
3228D ILE* 1.3 62.2 + - - +
3229D GLY* 3.5 26.8 + - - +
3230D ALA* 3.5 27.9 - - - +
3237D VAL* 4.1 2.6 - - - +
3239D GLY 4.0 1.4 + - - -
3240D SER* 3.0 23.7 + - - +
3241D GLU 3.6 6.1 - - - +
3242D THR* 4.7 3.4 - - - +
3264D TYR* 3.6 8.9 + - - -
3502D ADP 5.2 1.0 + - - -
4255D PHE* 3.5 34.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3226D ARG* 3.9 10.1 - - + +
3227D ARG* 1.3 77.5 - - - +
3229D GLY* 1.3 58.7 + - - +
3241D GLU* 2.8 37.5 + - + +
3242D THR 4.2 4.5 - - - +
3243D ARG* 3.6 55.0 - - + +
3259D GLU* 4.0 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232A LYS* 6.1 2.9 - - - -
3227D ARG* 3.5 22.6 - - - +
3228D ILE* 1.3 81.7 - - - +
3230D ALA* 1.3 58.0 + - - -
3240D SER* 3.7 0.3 - - - -
3241D GLU* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3227D ARG* 3.5 24.8 - - - +
3229D GLY* 1.3 74.4 - - - -
3231D VAL* 1.3 62.0 + - - +
3232D LYS* 3.6 23.6 + - + +
3237D VAL* 4.0 16.8 - - + -
3239D GLY 3.7 0.4 - - - -
3241D GLU* 4.5 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3230D ALA* 1.3 69.0 - - - +
3232D LYS* 1.3 64.6 + - - +
3237D VAL* 3.7 2.6 - - - -
3238D VAL* 2.9 43.3 + - + +
3239D GLY* 2.8 32.0 + - - +
3240D SER 4.0 1.6 - - - +
3241D GLU* 3.4 30.7 - - - +
3261D GLN* 3.5 30.7 - - + +
3263D LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232A LYS* 6.6 0.2 - - - +
3230D ALA* 3.6 18.4 + - + +
3231D VAL* 1.3 80.6 - - - +
3233D GLU* 1.3 62.9 + - - +
3234D GLY* 3.5 21.1 + - - +
3235D GLU 4.8 3.8 - - - +
3236D ASN 3.2 10.8 - - - +
3237D VAL* 4.2 17.5 - - + -
3238D VAL* 4.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1289A ALA* 4.5 16.8 - - - +
1300A GLN* 5.8 1.0 - - - +
1301A GLY* 3.8 25.9 + - - -
1302A LYS* 4.7 4.8 + - - +
3231D VAL 4.3 0.2 + - - -
3232D LYS* 1.3 72.2 - - - +
3234D GLY* 1.3 52.7 + - - +
3235D GLU* 2.7 16.7 + - - +
3236D ASN* 2.7 35.9 + - + +
3238D VAL* 3.9 25.4 - - + -
----------------------------------------------------------
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