Contacts of the strand formed by residues 3219 - 3233 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3061A ILE* 3.3 14.0 - - - +
3063A GLU* 4.3 10.8 - - + +
3215A LEU* 2.9 20.7 + - + +
3216A LYS 4.2 0.4 - - - +
3217A PHE 3.4 0.7 - - - +
3218A TYR* 1.3 77.3 - - - +
3220A SER* 1.3 60.7 + - - +
3221A VAL 3.7 8.1 - - - +
3222A ARG* 3.7 29.8 - - + -
3248A LYS* 3.0 28.5 + - - -
3250A LYS* 4.1 2.1 - - - +
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Residues in contact with SER3220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2098A ALA* 4.7 2.6 - - - +
3057A PRO* 4.4 8.7 - - - -
3060A ARG* 3.0 52.0 + - - +
3061A ILE 2.7 11.6 + - - -
3218A TYR 3.4 5.7 + - - -
3219A ALA* 1.3 73.7 - - - +
3221A VAL* 1.3 63.5 + - - +
3248A LYS* 4.5 2.4 - - - +
3249A ASN* 3.5 1.6 + - - -
3250A LYS* 2.8 45.1 + - - +
3251A ILE* 4.5 1.7 + - - -
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Residues in contact with VAL3221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3051A LEU* 3.6 21.1 - - + -
3056A LEU* 4.1 8.3 - - + -
3057A PRO* 4.0 24.7 - - + -
3061A ILE 3.8 2.0 + - - -
3062A VAL* 3.4 16.3 - - + +
3063A GLU 3.0 23.0 + - - -
3219A ALA* 3.7 1.4 - - - +
3220A SER* 1.3 86.2 - - - +
3222A ARG* 1.3 67.5 + - - +
3223A LEU* 3.5 27.1 - - + -
3246A VAL* 4.6 0.9 - - + -
3248A LYS 3.2 7.9 - - - +
3249A ASN* 3.7 17.3 - - - +
3251A ILE* 4.8 3.8 - - + -
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Residues in contact with ARG3222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2068A GLU* 4.4 10.7 + - - -
3063A GLU* 2.4 51.4 + - + +
3065A TYR* 3.7 30.4 + - + -
3209A THR* 4.4 7.9 + - - +
3216A LYS* 4.0 43.7 + - - +
3219A ALA* 3.7 19.7 - - + -
3221A VAL* 1.3 78.8 - - - +
3223A LEU* 1.3 66.6 + - - +
3246A VAL* 3.6 0.5 - - - -
3247A VAL* 2.8 41.4 + - + +
3248A LYS* 2.9 35.0 + - + +
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Residues in contact with LEU3223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3047A LEU* 4.5 17.7 - - + -
3051A LEU* 4.3 3.4 - - + -
3056A LEU* 4.3 22.0 - - + -
3062A VAL* 4.6 2.2 - - + -
3063A GLU 2.7 11.4 + - - +
3064A ILE* 3.4 31.1 - - + -
3065A TYR* 2.8 37.6 + - - +
3075A LEU* 4.9 4.9 - - + -
3221A VAL* 3.5 19.5 - - + -
3222A ARG* 1.3 81.3 - - - +
3224A ASP* 1.3 57.1 + - - +
3225A ILE 3.8 0.4 + - - -
3244A VAL* 3.6 20.9 - - + -
3245A LYS 3.5 1.8 - - - +
3246A VAL* 4.0 26.0 - - + -
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Residues in contact with ASP3224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3065A TYR* 3.5 29.9 + - + +
3066A GLY* 4.9 0.2 - - - -
3207A GLU* 5.0 0.3 - - - +
3222A ARG 4.2 0.6 + - - -
3223A LEU* 1.3 69.8 - - - +
3225A ILE* 1.3 62.0 + - - +
3226A ARG* 2.7 41.0 + - - -
3243A ARG 3.6 1.7 - - - +
3244A VAL* 3.3 3.5 - - - -
3245A LYS* 2.8 48.7 + - + +
3247A VAL* 3.5 23.8 - - + +
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Residues in contact with ILE3225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3064A ILE* 3.8 13.9 - - + -
3065A TYR 2.9 18.1 + - - +
3066A GLY* 3.4 2.6 - - - -
3067A PRO* 3.4 14.4 - - - +
3070A SER* 3.6 26.1 - - - +
3071A GLY* 3.8 19.1 - - - +
3072A LYS* 3.6 26.7 - - + -
3075A LEU* 4.0 15.0 - - + -
3223A LEU 3.8 0.6 - - - -
3224A ASP* 1.3 73.7 - - - +
3226A ARG* 1.3 72.1 + - - +
3242A THR* 3.7 22.0 - - + -
3243A ARG 3.5 2.9 - - - -
3244A VAL* 3.8 19.7 - - + +
3260A PHE* 4.6 0.9 - - + -
3262A ILE* 4.8 2.2 - - + -
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Residues in contact with ARG3226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3065A TYR* 4.6 1.6 - - - -
3067A PRO* 3.4 25.3 - - + +
3070A SER* 4.2 8.7 - - - -
3195A ILE* 3.2 19.3 - - - +
3207A GLU* 2.7 41.2 + - - -
3224A ASP* 2.7 34.7 + - - -
3225A ILE* 1.3 80.1 - - - +
3227A ARG* 1.3 66.3 + - - +
3228A ILE* 3.6 9.7 + - + +
3242A THR* 3.6 2.6 - - - +
3243A ARG* 2.9 38.4 + - + +
3245A LYS* 5.9 5.6 - - - +
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Residues in contact with ARG3227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3067A PRO* 5.5 1.4 - - - +
3068A GLU 6.0 0.4 - - - +
3069A SER* 4.6 7.4 - - - +
3070A SER* 4.2 21.2 - - - +
3226A ARG* 1.3 75.0 - - - +
3228A ILE* 1.3 63.7 + - - +
3229A GLY* 3.5 27.0 + - - +
3230A ALA* 3.5 27.1 - - - +
3237A VAL* 4.0 0.6 - - - +
3239A GLY 4.0 1.6 + - - -
3240A SER* 3.0 23.4 + - - +
3241A GLU 3.6 7.2 - - - +
3242A THR* 4.7 3.1 - - - +
3264A TYR* 3.6 10.1 + - - -
3502A ADP 5.1 0.8 + - - -
4255A PHE* 3.3 39.3 - - - -
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Residues in contact with ILE3228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3226A ARG* 3.8 10.1 - - + +
3227A ARG* 1.3 77.2 - - - +
3229A GLY* 1.3 59.7 + - - +
3241A GLU* 2.8 37.5 + - + +
3242A THR 4.2 4.5 - - - +
3243A ARG* 3.6 54.5 - - + +
3259A GLU* 4.0 21.8 - - + +
1232D LYS* 5.5 1.0 + - - -
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Residues in contact with GLY3229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3227A ARG* 3.5 22.8 - - - +
3228A ILE* 1.3 82.1 - - - +
3230A ALA* 1.3 57.1 + - - -
3240A SER* 3.7 0.2 - - - -
3241A GLU* 2.8 36.9 + - - +
1232D LYS* 4.6 11.0 - - - -
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Residues in contact with ALA3230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3227A ARG* 3.5 24.1 - - - +
3229A GLY* 1.3 73.9 - - - -
3231A VAL* 1.3 62.6 + - - +
3232A LYS* 3.6 23.4 + - + +
3237A VAL* 4.0 17.3 - - + -
3239A GLY 3.7 0.4 - - - -
3241A GLU* 4.5 4.1 - - - +
1232D LYS* 4.5 15.5 + - - +
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Residues in contact with VAL3231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3230A ALA* 1.3 68.6 - - - +
3232A LYS* 1.3 64.7 + - - +
3237A VAL* 3.7 2.6 - - - -
3238A VAL* 2.9 43.5 + - + +
3239A GLY* 2.8 30.7 + - - +
3240A SER 4.0 1.3 - - - +
3241A GLU* 3.4 32.3 - - - +
3261A GLN* 3.6 28.9 - - + +
3263A LEU* 4.0 12.6 - - + -
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Residues in contact with LYS3232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3230A ALA* 3.6 17.9 + - + +
3231A VAL* 1.3 80.7 - - - +
3233A GLU* 1.3 62.9 + - - +
3234A GLY* 3.5 22.3 + - - +
3235A GLU 4.8 3.6 - - - +
3236A ASN 3.2 10.5 - - - +
3237A VAL* 4.2 17.5 - - + -
3238A VAL* 4.7 1.1 - - - +
1229D GLY* 5.3 5.5 - - - -
1230D ALA 4.3 20.0 + - - +
1232D LYS* 6.5 0.9 - - - +
1241D GLU* 5.1 11.5 + - - +
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Residues in contact with GLU3233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3232A LYS* 1.3 72.2 - - - +
3234A GLY* 1.3 51.8 - - - +
3235A GLU* 2.7 16.9 + - - +
3236A ASN* 2.7 36.4 + - + +
3238A VAL* 3.9 26.2 - - + -
1291D TYR* 4.6 4.3 + - - -
1301D GLY* 4.6 5.8 - - - -
1302D LYS* 3.7 42.4 + - - +
1303D ALA 5.6 0.5 + - - -
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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