Contacts of the strand formed by residues 3134 - 3145 (chain D) in PDB entry 1W21
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 GLY3134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2216C GLY 5.8 2.7 - - - -
2217C ARG* 3.6 16.3 - - - +
3130D CYS* 3.1 4.4 - - - +
3131D ASP* 2.8 36.9 + - - +
3132D PRO 3.5 0.2 - - - -
3133D GLN* 1.3 80.4 - - - +
3135D CYS* 1.3 63.7 + - - -
3136D ARG* 5.7 0.9 - - - -
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Residues in contact with CYS3135 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2217C ARG* 6.5 0.2 - - - -
3106D LEU* 5.5 3.8 - - - -
3128D LEU* 5.1 0.9 - - + -
3129D SER 3.7 4.7 - - - +
3130D CYS* 2.1 45.3 - - - -
3134D GLY* 1.3 75.2 - - - -
3136D ARG* 1.3 69.4 + - - +
3168D GLU* 5.1 1.6 - - - +
3169D MET* 3.4 45.1 + - + +
3416D PHE* 4.7 8.3 - - + -
3418D ASP* 4.1 16.2 - - - -
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Residues in contact with ARG3136 (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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3128D LEU* 3.3 9.3 - - - +
3129D SER 3.0 32.2 + - - +
3131D ASP* 4.7 14.1 - - - -
3134D GLY 5.7 0.7 - - - -
3135D CYS* 1.3 78.0 - - - +
3137D MET* 1.3 64.9 + - - +
3138D PHE* 3.7 17.3 - - + -
3166D SER* 2.9 43.6 + - - -
3167D TRP* 3.4 15.8 - - - +
3168D GLU* 3.7 21.5 - - - +
3169D MET 4.1 2.2 - - - +
3177D ASN 5.5 0.6 + - - -
3179D ARG* 3.5 39.0 - - - +
3181D GLU* 5.0 0.2 + - - -
3196D ARG* 5.7 4.9 - - - +
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Residues in contact with MET3137 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3107D SER* 3.3 34.1 - - - +
3108D LYS 4.6 1.1 - - - +
3109D ASP* 4.1 15.5 - - + +
3127D TYR 3.5 4.3 - - - +
3128D LEU* 3.5 18.2 - - + -
3136D ARG* 1.3 71.0 - - - +
3138D PHE* 1.3 66.3 + - - +
3166D SER* 3.1 4.9 - - - -
3167D TRP* 2.9 67.0 + - + +
3169D MET* 4.1 6.5 - - + +
3170D GLY* 3.4 19.5 - - - +
3171D GLN 3.9 4.7 - - - +
3451D ILE* 4.0 33.9 - - + -
3453D ALA* 5.6 0.7 - - + -
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Residues in contact with PHE3138 (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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3126D PRO* 3.1 3.6 - - - +
3127D TYR* 2.7 69.6 + + + +
3129D SER* 3.6 29.4 - - - -
3136D ARG* 3.7 26.9 - - + -
3137D MET* 1.3 76.6 - - - +
3139D ALA* 1.3 64.7 + - - +
3164D LEU* 4.0 11.7 - - + -
3165D ILE 3.2 6.7 - - - -
3166D SER* 3.6 23.8 - - - -
3167D TRP* 3.7 5.5 - - - -
3181D GLU* 3.8 16.2 - - + -
3189D SER* 3.6 17.7 - - - -
3196D ARG* 3.6 28.0 - - - -
3451D ILE* 4.4 0.5 - - - +
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Residues in contact with ALA3139 (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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3123D THR* 3.9 22.4 - - + +
3124D ARG 3.9 1.1 - - - +
3125D GLU 3.8 9.9 - - - -
3126D PRO* 3.7 15.9 - - + -
3138D PHE* 1.3 79.8 - - - +
3140D LEU* 1.3 63.8 + - - +
3141D SER 3.7 0.2 - - - -
3164D LEU* 3.5 6.5 - - - +
3165D ILE* 2.9 35.8 + - - +
3167D TRP* 3.7 18.3 - - + -
3451D ILE* 5.3 0.2 - - + -
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Residues in contact with LEU3140 (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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3123D THR* 3.3 3.5 - - - -
3124D ARG 3.0 24.3 + - - +
3125D GLU* 3.7 32.1 + - + +
3127D TYR* 6.1 0.4 - - + -
3139D ALA* 1.3 72.9 - - - +
3141D SER* 1.3 59.6 + - - +
3162D ARG* 2.8 37.6 + - - +
3163D ALA 3.4 2.2 - - - +
3164D LEU* 4.0 24.0 - - - +
3184D GLY 4.1 13.2 - - - +
3185D TRP* 3.4 30.1 - - - +
3186D SER* 3.8 8.3 - - - +
3187D SER* 4.1 22.7 - - - +
3200D CYS* 5.4 0.4 - - - -
3234D GLU* 4.0 6.5 - - - +
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Residues in contact with SER3141 (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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3121D LEU* 4.0 17.9 - - - +
3122D VAL 3.4 11.4 + - - -
3123D THR* 4.2 3.1 - - - -
3139D ALA 3.5 3.6 + - - -
3140D LEU* 1.3 76.8 - - - +
3142D GLN* 1.3 60.5 + - - +
3143D GLY* 3.1 16.5 + - - -
3161D PHE 5.3 0.7 - - - -
3162D ARG* 3.1 27.3 + - - -
3163D ALA* 2.9 20.4 + - - -
3165D ILE* 4.0 25.6 - - - +
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Residues in contact with GLN3142 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113B ARG* 2.8 25.6 + - - -
3122D VAL* 2.9 43.9 + - + +
3123D THR* 4.8 2.4 + - - +
3124D ARG* 5.4 3.2 - - - +
3141D SER* 1.3 71.0 - - - +
3143D GLY* 1.3 56.8 + - - +
3144D THR* 3.4 0.7 - - + -
3154D THR* 3.1 30.3 + - + -
3155D ILE 5.1 0.2 - - - -
3156D HIS 3.1 25.2 + - - +
3158D ARG 6.0 0.2 - - - -
3159D SER* 4.3 0.5 + - - -
3161D PHE 3.4 9.6 - - - +
3162D ARG* 3.3 43.1 + - - +
3447D THR 5.4 0.8 + - - -
4479D GOL 2.7 35.0 + - - -
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Residues in contact with GLY3143 (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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1110B ASN* 4.4 8.4 - - - +
1113B ARG* 2.9 35.2 + - - +
1114B ILE* 3.8 17.0 - - - +
3141D SER* 3.1 12.8 + - - -
3142D GLN* 1.3 79.5 - - - +
3144D THR* 1.3 58.8 + - - +
3161D PHE 3.4 14.7 + - - -
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Residues in contact with THR3144 (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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1113B ARG* 3.9 10.5 + - - +
1114B ILE* 4.1 12.7 - - - +
3121D LEU* 3.3 11.1 - - - +
3122D VAL* 2.8 35.5 + - + +
3142D GLN* 3.9 4.5 - - + +
3143D GLY* 1.3 80.5 - - - +
3145D THR* 1.3 76.3 + - - +
3148D GLY* 4.5 3.1 - - - -
3150D HIS* 3.4 44.9 + - - +
3151D ALA* 3.4 11.9 + - - +
3154D THR* 4.0 7.4 - - + -
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Residues in contact with THR3145 (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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1113B ARG 5.4 0.6 + - - -
1114B ILE* 4.6 8.9 + - + +
1117B ASP* 2.8 32.9 + - - +
1118B ALA* 4.1 16.8 - - + -
3118D ALA 5.6 0.2 - - - -
3119D HIS* 4.2 9.9 - - + -
3120D ILE 3.1 17.5 - - - +
3121D LEU* 4.7 0.9 - - + -
3122D VAL* 3.6 2.2 - - - +
3144D THR* 1.3 90.2 + - - +
3146D LEU* 1.3 66.6 + - - +
3147D ARG 4.3 0.9 - - - -
3148D GLY* 3.2 13.7 + - - -
3151D ALA* 3.5 7.1 - - - +
3175D PRO* 4.1 26.2 - - + -
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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