Contacts of the strand formed by residues 3236 - 3249 (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 ASN3236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1286A LYS* 4.8 12.7 + - - +
1288A GLY 5.1 4.9 - - - +
3232D LYS* 3.2 6.1 - - - +
3233D GLU* 2.7 50.7 + - + +
3235D GLU* 1.3 88.2 - - - +
3237D VAL* 1.3 64.7 + - - +
3238D VAL* 3.7 4.0 - - + +
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Residues in contact with VAL3237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3227D ARG* 4.1 2.0 - - - +
3230D ALA* 4.0 18.2 - - + -
3231D VAL 3.7 3.4 - - - +
3232D LYS* 4.2 16.8 - - + -
3235D GLU 4.8 2.9 - - - +
3236D ASN* 1.3 75.1 - - - +
3238D VAL* 1.3 60.2 + - - +
3239D GLY 3.9 17.0 - - - +
3264D TYR* 3.7 13.2 - - + -
4253D ALA* 5.6 1.7 - - - +
4254D PRO 4.4 6.8 - - - +
4255D PHE* 3.7 44.8 + - + +
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Residues in contact with VAL3238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3231D VAL* 2.9 31.9 + - + +
3232D LYS 4.7 0.7 - - - -
3233D GLU* 3.9 30.7 - - + -
3236D ASN* 3.6 5.5 + - + +
3237D VAL* 1.3 72.3 - - - +
3239D GLY* 1.3 57.7 + - - +
3263D LEU* 3.8 13.3 - - + +
3264D TYR* 3.1 32.7 + - + +
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Residues in contact with GLY3239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3230D ALA* 3.7 4.9 - - - -
3231D VAL* 2.8 39.6 + - - +
3237D VAL* 3.9 3.8 - - - +
3238D VAL* 1.3 81.7 - - - +
3240D SER* 1.3 58.5 + - - -
3262D ILE 3.1 12.8 - - - -
3263D LEU* 4.1 2.7 - - - -
3264D TYR* 3.5 20.6 + - - -
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Residues in contact with SER3240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3069D SER 4.9 2.0 + - - -
3070D SER 5.7 2.0 - - - -
3227D ARG* 3.0 29.7 + - - +
3229D GLY 3.7 3.8 - - - -
3231D VAL* 4.0 3.1 - - - -
3239D GLY* 1.3 71.0 - - - -
3241D GLU* 1.3 61.2 + - - +
3242D THR* 3.4 10.0 + - - -
3261D GLN* 3.6 1.0 - - - -
3262D ILE* 2.8 46.1 + - - -
3264D TYR* 2.7 25.3 + - - -
3502D ADP 3.5 12.7 + - - -
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Residues in contact with GLU3241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234A GLY* 5.2 11.9 - - - -
3227D ARG* 3.6 2.9 - - - -
3228D ILE* 2.8 42.9 + - + -
3229D GLY* 2.8 31.5 + - - +
3230D ALA 4.4 3.6 - - - +
3231D VAL* 3.4 12.9 - - + +
3240D SER* 1.3 71.6 - - - +
3242D THR* 1.3 59.9 + - - +
3259D GLU* 5.6 3.0 - - + +
3260D PHE* 3.8 10.7 + - - +
3261D GLN* 3.2 38.9 + - - +
3302D LYS* 6.0 0.3 - - - -
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Residues in contact with THR3242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3070D SER 4.2 5.8 + - - +
3225D ILE* 3.7 28.5 - - + -
3226D ARG 3.6 6.5 + - - +
3227D ARG* 4.8 0.7 - - - -
3228D ILE* 4.4 4.4 - - - +
3240D SER* 3.4 18.4 + - - -
3241D GLU* 1.3 75.8 + - - +
3243D ARG* 1.3 64.4 + - - +
3244D VAL 4.4 0.2 - - - -
3258D ALA 4.5 0.2 - - - -
3259D GLU* 3.2 7.3 - - - +
3260D PHE* 2.7 72.5 + - + -
3262D ILE* 3.6 13.7 - - + +
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Residues in contact with ARG3243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3224D ASP 3.7 1.9 - - - +
3225D ILE* 3.5 1.2 - - - -
3226D ARG* 2.9 39.1 + - + +
3228D ILE* 3.6 40.4 - - + +
3242D THR* 1.3 75.2 - - - +
3244D VAL* 1.3 69.3 + - - +
3245D LYS* 4.1 21.8 - - - +
3257D GLN* 3.3 31.3 + - - +
3258D ALA 3.3 4.5 - - - +
3259D GLU* 2.4 43.5 + - + -
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Residues in contact with VAL3244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3047D LEU* 4.3 20.4 - - + +
3064D ILE* 6.1 0.2 - - + -
3075D LEU* 4.3 6.7 - - + -
3223D LEU* 3.6 36.1 - - + -
3224D ASP 3.4 6.7 - - - +
3225D ILE* 3.8 25.1 - - + -
3242D THR* 4.3 0.2 - - + -
3243D ARG* 1.3 78.3 - - - +
3245D LYS* 1.3 66.0 + - - +
3246D VAL* 5.2 1.2 - - - +
3257D GLN* 3.3 5.7 - - - +
3258D ALA* 2.7 37.2 + - + +
3260D PHE* 3.7 27.6 - - + -
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Residues in contact with LYS3245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3223D LEU* 3.5 4.5 - - - -
3224D ASP* 2.8 52.5 + - + +
3226D ARG* 5.8 5.5 - - - +
3243D ARG* 4.1 18.2 - - - +
3244D VAL* 1.3 74.1 - - - +
3246D VAL* 1.3 61.8 + - - +
3247D VAL* 3.3 12.7 + - + -
3255D PHE* 6.1 4.9 - - + +
3256D LYS 4.0 3.8 - - - +
3257D GLN* 3.5 35.2 - - + +
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Residues in contact with VAL3246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3047D LEU* 4.3 8.5 - - + -
3050D ALA* 4.1 28.9 - - + +
3051D LEU* 4.4 7.9 - - + +
3221D VAL* 4.7 0.2 - - + -
3222D ARG 3.7 4.9 - - - +
3223D LEU* 4.0 17.3 - - + -
3244D VAL 5.2 0.9 - - - +
3245D LYS* 1.3 72.2 - - - +
3247D VAL* 1.3 60.5 + - - +
3248D LYS 3.6 19.7 - - - +
3249D ASN* 3.9 26.5 - - + +
3254D PRO* 4.5 2.9 - - + -
3255D PHE* 2.8 36.4 + - - +
3256D LYS 3.0 21.3 + - - +
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Residues in contact with VAL3247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2069D SER* 6.2 0.2 - - - -
3065D TYR* 3.5 26.2 - - + +
3222D ARG* 2.8 30.5 + - + +
3224D ASP* 3.6 24.7 - - + +
3245D LYS* 3.9 13.0 - - + +
3246D VAL* 1.3 74.7 - - - +
3248D LYS* 1.3 60.8 + - + +
3254D PRO* 4.5 1.5 - - - +
3255D PHE* 3.5 30.2 - - + -
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Residues in contact with LYS3248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2068D GLU* 3.8 8.2 - - + +
2069D SER* 3.3 23.1 - - - +
2501D ALF 2.8 31.9 - - - -
3216D LYS 2.7 28.5 + - - +
3217D PHE 2.8 23.2 + - - -
3219D ALA 2.9 20.9 + - - +
3220D SER 4.8 1.1 - - - +
3221D VAL* 3.2 5.0 - - - -
3222D ARG* 2.9 48.4 + - + +
3246D VAL* 3.6 8.8 - - - +
3247D VAL* 1.3 81.3 - - + +
3249D ASN* 1.3 67.7 + - - +
3250D LYS* 4.5 6.3 - - - -
3254D PRO* 4.4 2.5 - - - -
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Residues in contact with ASN3249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2069D SER* 5.2 0.7 - - - -
2502D ADP 2.9 30.5 + - - -
3051D LEU* 3.2 28.3 + - - +
3220D SER 3.5 2.0 - - - -
3221D VAL* 3.7 9.9 - - - +
3246D VAL* 3.9 12.2 - - + +
3248D LYS* 1.3 80.8 - - - +
3250D LYS* 1.3 61.4 + - - +
3251D ILE* 3.0 28.6 + - - +
3252D ALA 3.1 30.3 + - - +
3253D ALA 3.3 12.1 + - - -
3254D PRO* 3.8 19.6 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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