Contacts of the strand formed by residues 129 - 139 (chain K) in PDB entry 1FSK
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 GLY 129 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124K GLN* 3.1 33.1 + - - +
125K LEU* 3.4 17.8 - - - +
127K SER* 3.1 5.0 + - - -
128K GLY* 1.3 81.8 - - - +
130K ALA* 1.3 62.7 + - - +
181K LEU 4.4 1.3 - - - -
183K LYS* 4.5 0.5 - - - +
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Residues in contact with ALA 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K PRO* 3.9 9.4 - - + -
124K GLN* 3.3 8.0 - - - +
125K LEU* 4.4 2.5 - - + -
129K GLY* 1.3 74.4 - - - +
131K SER* 1.3 58.8 + - - +
132K VAL* 4.2 0.6 + - - -
179K LEU 3.7 1.2 - - - +
180K THR* 3.3 3.4 - - - +
181K LEU* 2.7 52.3 + - + +
183K LYS* 4.0 6.7 - - - +
186K TYR* 3.7 35.0 - - + -
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Residues in contact with SER 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K PHE 4.0 1.0 - - - +
119K PRO 4.1 0.2 - - - -
120K PRO* 3.2 26.2 - - - +
124K GLN* 2.7 34.4 + - - +
130K ALA* 1.3 71.9 - - - +
132K VAL* 1.3 61.3 + - - +
133K VAL* 4.0 4.9 + - - +
178K THR* 4.6 3.8 - - - -
179K LEU 3.1 2.7 - - - -
180K THR* 2.9 31.0 + - - +
129L LEU* 5.5 3.6 - - - +
146L LEU* 4.3 19.9 - - - +
148L LYS* 4.0 7.1 + - - -
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Residues in contact with VAL 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K ILE* 3.9 4.0 - - + -
118K PHE 3.1 17.3 - - - +
120K PRO* 3.5 22.4 - - + -
130K ALA 5.2 1.8 - - - +
131K SER* 1.3 73.8 - - - +
133K VAL* 1.3 59.0 + - - +
148K TRP* 3.5 30.1 - - + -
178K THR* 3.3 0.9 - - - -
179K LEU* 2.5 52.0 + - + +
181K LEU* 5.7 2.5 - - + -
186K TYR* 4.4 13.7 - - + -
192K TYR* 4.7 11.4 - - + -
209K PHE* 3.7 23.8 - - + -
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Residues in contact with VAL 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K ILE* 3.5 4.0 - - - +
118K PHE* 2.8 51.4 + - + +
131K SER 4.6 5.2 - - - +
132K VAL* 1.3 79.9 - - - +
134K CYS* 1.3 63.8 + - - +
135K PHE* 4.3 13.5 - - + -
148K TRP* 3.9 0.9 - - - -
176K SER* 5.9 0.4 - - - +
177K SER 3.7 5.2 - - - +
178K THR* 3.8 21.3 - - + +
129L LEU* 3.1 37.9 - - + -
146L LEU* 4.1 20.4 - - + -
183L SER* 5.6 2.9 - - - -
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Residues in contact with CYS 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K VAL* 3.1 30.3 - - - -
116K SER 3.0 13.9 - - - -
117K ILE* 4.1 1.8 - - - -
133K VAL* 1.3 80.1 - - - +
135K PHE* 1.3 63.0 + - - +
136K LEU* 3.5 6.2 - - - +
148K TRP* 3.7 10.5 - - + -
176K SER* 3.4 4.3 - - - -
177K SER* 2.9 30.3 + - - +
194K CYS* 2.7 44.2 - - + -
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Residues in contact with PHE 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K THR 3.0 4.4 - - - +
115K VAL* 3.0 25.1 - - - -
116K SER* 2.9 16.4 + - - +
118K PHE* 3.8 29.2 - + - -
133K VAL* 4.3 9.2 - - + -
134K CYS* 1.3 75.2 - - - +
136K LEU* 1.3 61.3 + - - +
137K ASN* 3.4 20.6 - - - +
175K MET 3.7 2.2 - - - -
176K SER* 3.7 26.0 - - - -
129L LEU* 4.1 20.2 - - + -
142L THR* 5.0 2.7 - - - -
143L LEU 3.6 13.9 - - - -
144L GLY* 4.6 0.7 - - - -
171L PHE* 4.4 7.9 - + - -
183L SER* 4.2 17.7 - - - -
184L SER 4.3 9.4 - - - -
185L SER* 3.3 34.8 - - - -
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Residues in contact with LEU 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K PRO* 3.8 17.7 - - + -
114K THR 3.9 3.4 - - - -
115K VAL* 4.4 11.0 - - + +
134K CYS* 3.5 17.9 - - - +
135K PHE* 1.3 77.2 - - - +
137K ASN* 1.3 60.0 + - - +
139K PHE* 3.0 16.1 - - + -
144K ILE* 3.8 21.3 - - + -
146K VAL* 3.1 36.3 - - + -
175K MET* 2.9 48.5 + - + +
176K SER* 4.5 0.9 - - - -
177K SER* 4.5 2.9 - - - +
194K CYS* 5.8 0.9 - - - -
196K ALA* 3.9 15.7 - - + -
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Residues in contact with ASN 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K PRO* 3.6 0.2 - - - +
114K THR* 3.0 39.0 + - + +
116K SER* 6.0 0.2 + - - -
135K PHE* 3.4 24.2 - - - +
136K LEU* 1.3 82.6 + - - +
138K ASN* 1.3 89.0 + - - +
139K PHE* 3.6 1.8 - - - -
174K SER* 3.7 11.2 - - - +
142L THR* 5.7 5.3 + - - +
169L HIS* 3.9 12.0 + - - +
171L PHE* 3.7 6.5 - - - -
185L SER* 3.2 25.7 + - - -
186L VAL 5.6 0.2 + - - -
187L THR* 5.1 7.3 + - - -
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Residues in contact with ASN 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K ALA* 3.9 10.2 - - - +
112K ALA 3.7 10.3 - - - +
114K THR* 5.0 6.7 + - - +
137K ASN* 1.3 94.4 + - - +
139K PHE* 1.3 60.8 + - - +
167K ASP* 5.3 1.0 - - - +
170K ASP* 3.6 10.5 - - - +
172K THR* 3.3 24.1 + - + +
173K TYR 2.7 18.4 + - - -
174K SER* 3.1 1.6 + - - -
169L HIS* 3.2 24.6 + - - -
187L THR* 5.9 0.4 + - - -
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Residues in contact with PHE 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K ALA* 3.4 17.7 - - - +
113K PRO* 3.7 24.7 - - + -
136K LEU* 3.0 35.4 - - + -
138K ASN* 1.3 75.0 - - - +
140K TYR* 1.3 67.8 + - - +
141K PRO 3.1 20.4 - - - -
142K LYS* 3.3 26.2 - - - -
144K ILE* 3.5 25.4 - - + -
163K TRP* 4.0 8.1 - + - -
172K THR* 3.1 20.4 - - - +
173K TYR* 3.1 16.3 + - + -
174K SER* 3.4 15.9 - - - -
175K MET* 3.6 15.0 - - + -
198K HIS* 3.7 9.9 - + - +
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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