Contacts of the strand formed by residues 117 - 130 (chain F) in PDB entry 1SID
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 LEU 117 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108F LEU 5.7 1.3 - - - +
109F ASN 3.8 10.1 - - - +
110F GLU* 4.5 7.9 - - + +
116F THR* 1.3 80.1 + - - +
118F GLN* 1.3 93.3 + - - +
119F MET* 4.2 26.0 - - + -
276F GLU* 5.4 6.7 - - - +
314F TRP* 3.1 7.2 - - - -
315F VAL* 2.6 46.0 + - + +
317F ASN* 4.3 14.6 - - + +
318F PRO* 4.2 21.5 - - + -
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Residues in contact with GLN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F GLY 4.4 1.7 - - - +
43F PRO* 4.4 13.7 - - - +
108F LEU* 3.0 45.1 - - + +
109F ASN* 3.0 37.6 + - - +
117F LEU* 1.3 87.9 - - - +
119F MET* 1.3 63.6 + - - +
276F GLU* 5.5 1.6 - - - +
312F LYS* 4.1 31.2 - - + +
313F ARG 3.4 8.5 - - - +
314F TRP* 3.1 37.6 + - + +
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Residues in contact with MET 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLY* 4.1 14.4 - - - -
363C ASP 6.1 0.2 - - - +
108F LEU* 3.9 9.2 - - - -
117F LEU* 4.1 17.0 - - + +
118F GLN* 1.3 77.9 - - - +
120F TRP* 1.3 64.2 + - - +
121F GLU* 3.4 2.3 + - - +
272F LEU* 4.5 15.0 - - + +
273F CYS 3.0 34.1 - - - +
274F LYS* 3.9 11.4 - - + -
275F GLY 5.2 1.8 - - - +
276F GLU* 4.8 9.2 - - - +
311F ARG 3.5 1.6 - - - +
312F LYS* 3.5 1.4 - - - -
313F ARG* 2.6 41.5 + - - +
315F VAL* 3.7 41.1 - - + -
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Residues in contact with TRP 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 5.6 4.0 - - + -
41F THR* 4.8 11.0 - - + -
45F SER 5.5 1.1 - - - -
47F THR* 4.2 21.5 - - - -
105F LEU* 3.2 33.4 - - + -
106F PRO* 3.0 38.9 + - + +
108F LEU* 2.9 40.6 - - + +
119F MET* 1.3 75.6 - - - +
121F GLU* 1.3 58.2 + - - +
272F LEU* 3.2 5.2 - - - +
273F CYS* 2.7 54.1 + - + +
276F GLU* 3.8 13.6 + - - -
310F LEU* 4.5 11.2 - - + -
311F ARG* 3.5 17.9 - - - -
312F LYS* 3.8 28.3 - - + -
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Residues in contact with GLU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F MET 4.3 4.0 - - - +
120F TRP* 1.3 75.0 - - - +
122F ALA* 1.3 61.9 + - - +
123F VAL* 3.4 13.2 - - - +
264F LEU* 4.1 1.7 - - - +
269F VAL 2.8 23.7 - - - +
271F PRO 2.9 19.3 - - - +
272F LEU* 4.2 8.5 - - + +
310F LEU* 2.8 22.0 - - - +
311F ARG* 2.7 64.9 + - + +
313F ARG* 2.7 42.8 + - + +
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F TRP 4.2 1.2 + - - -
121F GLU* 1.3 74.1 - - - +
123F VAL* 1.3 62.6 + - - +
167F VAL* 4.2 10.3 - - + -
168F GLY 5.9 0.2 - - - +
263F LEU* 3.8 12.3 - - + -
269F VAL 3.8 0.3 - - - +
270F GLY* 3.5 7.3 - - - -
271F PRO* 2.8 53.3 + - + +
273F CYS* 4.6 7.5 - - - -
278F LEU* 5.2 2.0 - - + -
308F ILE* 4.3 6.5 - - + -
309F THR 4.1 0.7 - - - -
310F LEU* 3.7 13.2 - - + +
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Residues in contact with VAL 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 6.4 0.4 - - + -
121F GLU* 3.4 25.6 - - - +
122F ALA* 1.3 80.4 - - - +
124F SER* 1.3 66.4 + - - +
262F VAL* 3.3 6.0 - - + +
263F LEU* 2.5 34.4 + - - +
264F LEU* 3.2 19.9 + - + +
309F THR* 2.8 19.9 + - + +
310F LEU* 4.1 3.1 - - - -
311F ARG* 3.9 21.1 - - + +
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Residues in contact with SER 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F VAL* 1.3 86.1 - - - +
125F VAL* 1.3 68.6 + - - +
260F THR* 3.9 16.4 - - - +
261F THR 2.9 15.3 - - - -
262F VAL* 4.4 5.4 - - - -
263F LEU* 3.3 7.8 - - - +
308F ILE* 3.5 0.3 - - - -
309F THR* 2.7 53.4 + - - +
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Residues in contact with VAL 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F SER* 1.3 80.3 + - - +
126F LYS* 1.3 74.9 + - - +
127F THR* 4.0 4.5 + - - -
165F PHE* 5.2 9.9 - - + -
167F VAL* 4.0 19.7 - - + -
240F PHE* 6.2 0.2 - - + -
260F THR* 4.1 0.6 - - - +
261F THR* 2.6 46.1 + - + +
263F LEU* 3.2 30.3 - - + -
306F PHE* 4.7 6.5 - - + -
307F LYS 3.1 13.7 - - - +
308F ILE* 4.1 11.9 - - + -
309F THR* 4.5 0.7 - - - -
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Residues in contact with LYS 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F VAL* 1.3 76.5 - - - +
127F THR* 1.3 63.0 + - - +
256F THR 5.8 2.5 - - - +
257F ASN 3.4 25.8 + - - +
258F THR* 3.8 12.1 + - - +
259F LEU 3.5 22.7 - - - +
260F THR* 3.5 30.3 + - + +
305F TYR* 4.0 7.8 - - + +
306F PHE* 3.5 0.9 - - - -
307F LYS* 2.7 69.8 + - + +
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Residues in contact with THR 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F VAL* 4.0 5.6 + - - -
126F LYS* 1.3 77.4 - - - +
128F GLU* 1.3 66.9 + - - +
165F PHE* 4.3 26.9 - - + -
256F THR 4.4 6.9 - - - +
259F LEU 4.6 3.4 + - - +
304F ARG* 3.0 39.0 - - - +
305F TYR* 2.4 24.3 + - - -
306F PHE* 4.0 6.1 - - - -
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F THR* 1.3 85.4 + - - +
129F VAL* 1.3 69.7 + - - +
130F VAL* 3.9 15.2 + - + +
254F GLN 3.9 8.7 - - - +
255F PHE* 3.7 16.8 - - - -
256F THR* 3.1 46.8 + - - +
257F ASN* 3.6 4.0 + - - -
304F ARG* 3.4 2.7 - - - +
305F TYR* 2.8 43.0 + - + +
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Residues in contact with VAL 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F GLU* 1.3 79.7 - - - +
130F VAL* 1.3 66.4 + - - +
132F SER* 3.8 4.0 + - - -
163F HIS* 4.9 5.2 - - + +
253F LEU* 3.7 33.7 - - + +
254F GLN 5.2 2.3 + - - +
255F PHE* 4.1 5.9 - - - -
284F ASP* 3.5 19.5 - - + +
286F MET* 5.3 1.8 - - - -
302F LEU* 3.5 25.4 - - + -
303F PRO 3.4 13.7 - - - +
304F ARG* 3.5 36.8 - - + +
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Residues in contact with VAL 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F GLU* 4.1 18.8 - - + +
129F VAL* 1.3 81.1 - - - +
131F GLY* 1.3 63.7 + - - +
132F SER 3.5 1.1 - - - -
255F PHE* 4.0 14.6 - - + -
302F LEU* 3.4 8.3 - - - +
303F PRO* 3.2 47.0 + - + +
304F ARG* 5.1 1.6 - - - -
305F TYR* 5.1 6.5 - - + +
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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