Contacts of the strand formed by residues 129 - 139 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124G GLN* 3.2 47.8 - - - +
125G LEU* 3.8 1.3 + - - -
127G SER 3.3 7.0 + - - -
128G GLY* 1.3 76.0 - - - +
130G ALA* 1.3 63.7 + - - +
180G THR* 3.5 30.3 - - + -
181G LEU 3.7 5.8 - - - +
182G SER* 4.8 0.7 - - - +
149H LYS* 4.1 13.1 + - - +
150H ASP* 5.6 1.0 + - - -
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Residues in contact with ALA 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G PRO* 3.9 15.3 - - + -
124G GLN* 3.6 4.3 - - - -
125G LEU* 3.5 29.6 - - + -
128G GLY 3.8 0.6 + - - -
129G THR* 1.3 73.4 - - - +
131G SER* 1.3 63.4 + - - +
132G VAL* 5.5 0.2 - - - -
179G LEU 3.9 0.9 - - - +
180G THR* 3.8 2.8 - - - +
181G LEU* 2.9 42.4 + - + +
183G LYS* 4.9 1.8 - - - -
186G TYR* 4.4 17.3 - - + -
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Residues in contact with SER 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G PRO 3.8 2.6 - - - +
120G PRO* 3.2 25.1 - - - +
124G GLN* 2.7 37.9 + - - -
130G ALA* 1.3 73.9 + - - +
132G VAL* 1.3 62.8 + - - +
133G VAL* 4.2 3.1 + - - +
178G THR* 4.3 14.3 - - - +
179G LEU 3.5 6.3 - - - -
180G THR* 4.4 5.6 + - - +
130H LEU* 5.7 2.3 - - - +
147H LEU* 3.9 19.2 - - - +
149H LYS* 3.6 13.2 - - - +
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Residues in contact with VAL 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ILE* 4.2 2.2 - - + -
118G PHE 3.2 17.0 - - - +
119G PRO* 4.4 0.2 - - + -
120G PRO* 4.3 10.5 - - + -
131G SER* 1.3 76.3 - - - +
133G VAL* 1.3 60.0 + - - +
148G TRP* 3.7 27.4 - - + -
178G THR* 3.5 4.2 - - - +
179G LEU* 3.0 52.7 + - + +
181G LEU* 4.5 13.0 - - + -
186G TYR* 4.6 7.6 - - + -
192G TYR* 4.6 7.0 - - + -
209G PHE* 3.6 26.7 - - + -
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ILE* 3.4 6.6 - - - +
118G PHE* 2.9 54.7 + - + +
131G SER 4.2 2.6 + - - +
132G VAL* 1.3 75.4 - - - +
134G CYS* 1.3 70.8 + - - +
135G LEU* 4.8 3.6 - - + -
148G TRP* 4.2 3.4 - - - -
176G SER* 5.6 5.2 - - - -
177G SER 3.4 3.1 - - - +
178G THR* 3.0 29.4 - - + +
130H LEU* 3.9 33.2 - - + -
147H LEU* 5.2 11.0 - - + -
185H SER* 5.0 9.4 - - - +
187H VAL* 5.8 2.5 - - + -
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Residues in contact with CYS 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G VAL* 4.3 5.2 - - - -
116G PHE 3.7 9.6 - - - -
117G ILE* 4.8 0.7 - - - +
133G VAL* 1.3 75.9 - - - +
135G LEU* 1.3 63.1 + - - +
136G LEU* 4.1 17.2 - - + +
146G VAL* 4.4 0.9 - - + -
148G TRP* 3.6 14.3 - - + -
175G LEU 3.8 0.7 - - - +
176G SER* 3.6 5.0 - - - -
177G SER* 2.7 45.0 + - - +
194G CYS* 2.0 52.5 - - - -
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Residues in contact with LEU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G SER 3.4 1.7 - - - +
115G VAL* 3.3 5.4 - - - -
116G PHE* 2.9 50.4 + - + +
118G PHE* 3.9 21.5 - - + -
133G VAL* 4.8 4.5 - - + -
134G CYS* 1.3 75.3 - - - +
136G LEU* 1.3 69.0 - - - +
137G ASN* 3.8 24.9 - - - +
174G SER* 4.8 0.2 - - - -
175G LEU 3.7 1.6 - - - +
176G SER* 5.8 0.2 - - - -
143H ALA* 4.3 17.9 - - + -
172H PHE* 4.1 25.6 - - + -
187H VAL* 3.8 33.0 - - + -
189H THR* 5.5 0.9 - - + -
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Residues in contact with LEU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G PRO* 4.3 8.1 - - + -
114G SER 3.9 4.0 - - - -
115G VAL* 4.0 8.5 - - + -
134G CYS* 4.1 14.8 - - + -
135G LEU* 1.3 83.2 - - - +
137G ASN* 1.3 60.1 + - - +
139G PHE* 3.8 19.9 - - + -
144G ALA* 4.4 20.2 - - + -
146G VAL* 4.5 12.1 - - + -
174G SER* 3.4 8.7 - - - -
175G LEU* 3.1 49.8 + - + +
177G SER* 6.5 0.4 - - - -
196G VAL* 3.9 39.7 - - + -
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Residues in contact with ASN 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G ALA 4.4 0.2 - - - +
114G SER* 3.0 48.4 + - - +
116G PHE* 4.4 7.4 - - + -
135G LEU* 3.8 20.4 - - + +
136G LEU* 1.3 72.5 - - - +
138G ASN* 1.3 86.4 + - - +
139G PHE* 3.9 1.5 - - - -
174G SER* 3.2 17.0 + - - -
170H HIS* 3.6 17.2 + - - -
187H VAL* 4.7 1.2 - - - +
189H THR* 3.1 30.9 + - - +
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Residues in contact with ASN 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G ALA* 4.5 3.1 - - - +
112G ALA 3.2 13.9 - - - +
137G ASN* 1.3 95.8 - - - +
139G PHE* 1.3 57.8 + - - +
167G ASP* 5.2 2.6 + - - +
170G ASP* 3.6 15.2 + - - +
172G THR* 3.2 32.2 + - + +
173G TYR 3.1 15.2 + - - -
174G SER* 3.2 4.1 + - - -
170H HIS* 3.4 22.8 + - - -
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Residues in contact with PHE 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G ALA 3.5 13.9 - - - +
113G PRO* 3.6 22.9 - - + -
136G LEU* 3.8 28.5 - - + -
138G ASN* 1.3 73.5 - - - +
140G TYR* 1.3 59.1 + - - +
141G PRO 3.2 20.0 - - - -
142G ARG* 3.2 33.9 - - + -
144G ALA* 4.4 7.2 - - + -
163G VAL* 5.2 0.4 - - + -
172G THR* 3.6 5.2 - - - -
173G TYR* 2.8 60.1 + - + -
174G SER* 3.9 0.7 - - - -
175G LEU* 3.8 39.9 - - + -
198G HIS* 3.5 11.7 - + - +
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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