Contacts of the strand formed by residues 129 - 139 (chain O) in PDB entry 3KYM
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 THR 129 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124O GLN* 3.0 43.2 - - - +
125O LEU* 3.7 4.6 + - - -
127O SER* 3.3 15.1 + - - -
128O GLY* 1.3 81.7 + - - +
130O ALA* 1.3 63.5 + - - +
180O THR* 4.6 12.8 - - + -
181O LEU 3.7 10.8 - - - +
182O SER* 4.4 0.7 - - - +
183O LYS* 4.3 0.9 - - - +
149P LYS* 4.1 19.1 - - + +
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Residues in contact with ALA 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O PRO* 4.0 11.9 - - + -
124O GLN* 3.5 5.8 - - - +
125O LEU* 3.7 23.3 - - + -
129O THR* 1.3 76.0 - - - +
131O SER* 1.3 58.5 + - - +
132O VAL* 4.9 1.9 - - + +
179O LEU 3.7 1.0 - - - +
180O THR* 3.8 2.6 - - - +
181O LEU* 2.7 46.8 + - + +
182O SER 4.4 1.3 - - - +
186O TYR* 4.0 24.5 - - + -
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Residues in contact with SER 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O PHE 4.2 0.3 - - - +
119O PRO 3.8 0.5 - - - -
120O PRO* 2.8 31.0 - - - +
124O GLN* 2.9 26.9 + - - +
130O ALA* 1.3 71.5 + - - +
132O VAL* 1.3 63.5 + - - +
133O VAL* 5.0 1.8 - - - +
178O THR* 3.8 15.2 - - - +
179O LEU 3.3 10.5 + - - -
180O THR* 4.4 6.8 + - - +
130P LEU* 6.1 0.3 - - - +
147P LEU* 3.8 21.6 - - - +
149P LYS* 4.0 13.3 - - - -
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Residues in contact with VAL 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ILE* 4.3 0.9 - - + -
118O PHE 3.4 15.5 - - - +
120O PRO* 3.9 12.1 - - + -
130O ALA 4.9 2.5 - - - +
131O SER* 1.3 79.2 - - - +
133O VAL* 1.3 64.1 + - - +
148O TRP* 3.9 24.2 - - + -
177O SER 3.6 0.7 - - - +
178O THR* 3.4 3.8 - - - +
179O LEU* 2.8 56.4 + - + +
181O LEU* 5.1 4.3 - - + -
186O TYR* 5.1 4.0 - - + -
192O TYR* 4.9 8.5 - - + -
209O PHE* 3.5 30.5 - - + -
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Residues in contact with VAL 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ILE* 3.4 2.1 - - - +
118O PHE* 2.7 56.6 + - + +
131O SER 5.0 0.9 - - - -
132O VAL* 1.3 81.1 - - - +
134O CYS* 1.3 68.6 + - - +
135O LEU* 4.8 3.6 - - + +
148O TRP* 4.2 3.1 - - - -
176O SER* 5.1 5.8 - - - -
177O SER 3.3 4.9 - - - +
178O THR* 3.8 20.9 - - + +
130P LEU* 3.8 35.0 - - + -
147P LEU* 4.4 14.4 - - + -
185P SER* 4.3 15.3 - - - +
187P VAL* 5.8 0.7 - - + -
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Residues in contact with CYS 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O VAL* 3.7 15.0 - - - -
116O PHE 3.3 12.8 - - - -
117O ILE* 4.5 0.2 - - - +
133O VAL* 1.3 74.5 - - - +
135O LEU* 1.3 60.0 + - - +
136O LEU* 3.9 11.1 + - + +
148O TRP* 3.6 12.7 - - + -
175O LEU 3.5 1.6 - - - +
176O SER* 3.2 7.4 - - - -
177O SER* 2.8 43.8 + - - -
194O CYS* 2.0 51.1 - - - -
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Residues in contact with LEU 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O SER 3.4 4.3 - - - +
115O VAL* 3.4 3.9 - - - -
116O PHE* 2.8 56.4 + - + +
118O PHE* 3.9 16.8 - - + -
133O VAL* 4.2 3.1 - - + -
134O CYS* 1.3 72.3 - - - +
136O LEU* 1.3 60.6 + - - +
137O ASN* 4.0 23.1 - - + +
174O SER* 5.7 0.2 - - - -
175O LEU 3.6 2.7 - - - +
176O SER* 4.9 3.8 - - - -
143P ALA* 3.9 16.2 - - + -
172P PHE* 3.6 33.0 - - + -
187P VAL* 3.6 32.8 - - + -
189P THR* 4.7 1.8 - - + -
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Residues in contact with LEU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O PRO* 3.7 17.0 - - + -
114O SER 3.9 2.7 - - - -
115O VAL* 4.5 7.6 - - + +
134O CYS* 3.9 28.7 - - + +
135O LEU* 1.3 72.3 - - - +
137O ASN* 1.3 59.6 + - - +
139O PHE* 3.6 7.0 - - + -
144O ALA* 4.1 22.2 - - + -
145O LYS 5.3 0.2 - - - +
146O VAL* 4.1 16.4 - - + -
174O SER* 3.5 2.9 - - - -
175O LEU* 2.7 67.2 + - + +
196O VAL* 3.8 34.8 - - + -
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Residues in contact with ASN 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O ALA 4.3 0.5 - - - +
113O PRO* 3.5 1.4 - - - +
114O SER* 3.1 42.8 + - - +
116O PHE* 4.0 12.1 - - + -
135O LEU* 4.0 16.1 - - + +
136O LEU* 1.3 74.5 - - - +
138O ASN* 1.3 95.2 + - - +
139O PHE* 3.7 2.7 - - - -
174O SER* 3.5 4.5 + - - -
170P HIS* 3.2 31.5 + - - -
187P VAL* 5.2 0.2 - - - +
189P THR* 3.9 26.4 + - - +
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Residues in contact with ASN 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O ALA* 3.9 13.2 - - - +
112O ALA 4.0 5.4 - - - +
137O ASN* 1.3 88.3 + - - +
139O PHE* 1.3 58.1 + - - +
170O ASP* 4.6 10.9 + - - +
172O THR* 3.7 22.4 + - + +
173O TYR 3.2 5.3 + - - -
174O SER* 2.9 13.8 + - - -
170P HIS* 2.8 33.0 + - - -
189P THR* 5.5 3.4 + - - -
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Residues in contact with PHE 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O ALA* 3.3 17.0 - - - +
113O PRO* 3.5 25.6 - - + -
136O LEU* 3.6 30.1 - - + -
138O ASN* 1.3 75.0 - - - +
140O TYR* 1.3 61.0 + - - +
141O PRO 3.2 28.7 - - - -
142O ARG* 3.7 17.9 - - + -
144O ALA* 3.9 18.8 - - + -
163O VAL* 5.5 2.0 - - + -
172O THR* 3.5 3.9 - - - -
173O TYR* 2.7 63.4 + - + -
174O SER* 3.9 1.3 - - - -
175O LEU* 3.8 26.2 - - + -
198O HIS* 3.4 13.0 - + - -
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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