Contacts of the strand formed by residues 120 - 133 (chain A) in PDB entry 4YCG
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 GLU 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ILE* 3.8 9.8 - - + +
87A ARG* 2.7 40.6 + - - -
116A ILE* 3.5 9.8 - - + +
117A PRO* 3.0 25.4 + - + +
118A ARG 3.6 3.6 - - - +
119A HIS* 1.3 88.1 - - + +
121A GLN* 1.3 60.3 + - - +
122A ILE* 4.0 2.4 + - - +
192A VAL* 5.3 5.5 - - - +
235A SER* 3.3 17.5 + - - +
236A ASN 3.5 6.7 - - - +
237A ASP* 4.5 1.3 - - - +
238A ARG* 3.5 15.4 + - - +
244A GLU* 3.3 4.8 - - - +
304A ZN 2.1 39.7 - - - -
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLU* 1.3 71.5 - - - +
122A ILE* 1.3 91.9 + - - +
123A THR* 3.8 7.4 + - + +
189A LYS* 5.1 8.3 - - - +
235A SER* 3.7 1.3 - - - -
236A ASN* 2.7 36.7 + - + +
237A ASP 5.1 0.4 - - - -
238A ARG* 2.8 50.5 + - + +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.7 31.9 - - + -
120A GLU 4.0 1.0 + - - +
121A GLN* 1.3 97.0 + - - +
123A THR* 1.3 61.8 + - - +
124A ARG 5.0 2.2 - - - +
125A ALA* 5.9 2.0 - - + -
185A SER 5.0 0.9 - - - +
188A VAL* 3.7 28.3 - - + -
189A LYS* 3.6 37.7 + - + -
192A VAL* 3.7 18.2 - - + -
233A VAL* 3.7 15.0 - - + -
234A PHE 3.4 8.7 - - - +
235A SER* 3.7 14.4 - - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 5.5 0.4 - - - +
83A SER* 2.7 23.2 + - - +
121A GLN* 3.9 10.3 - - + +
122A ILE* 1.3 77.3 - - - +
124A ARG* 1.3 65.6 + - - +
185A SER* 4.0 5.7 + - - -
189A LYS* 4.1 17.5 + - - +
234A PHE* 2.7 15.6 + - - +
236A ASN* 3.7 29.2 - - + +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 5.7 2.2 - - - -
123A THR* 1.3 85.2 + - - +
125A ALA* 1.3 66.0 + - - +
126A GLU* 3.1 34.5 + - - +
181A THR* 4.6 8.1 - - - +
183A GLU* 3.2 33.4 + - - +
185A SER* 3.3 12.6 - - - +
233A VAL* 3.6 2.6 - - - +
234A PHE* 2.6 57.2 + - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 5.9 1.3 - - + -
124A ARG* 1.3 76.6 - - - +
126A GLU* 1.3 64.0 + - - +
183A GLU* 3.7 5.5 - - - -
184A VAL* 3.2 23.7 + - - +
185A SER* 2.9 23.2 + - - +
188A VAL* 3.6 35.9 - - + -
231A PHE* 4.3 6.3 - - + -
232A VAL 3.4 6.3 - - - +
233A VAL* 4.6 5.2 - - + -
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 2.8 37.1 + - - -
124A ARG* 3.1 39.9 + - - +
125A ALA* 1.3 77.8 - - - +
127A LEU* 1.3 60.8 + - - +
128A ARG* 3.9 4.1 + - + -
181A THR* 3.6 26.8 - - + +
182A LEU 3.5 3.1 - - - +
183A GLU* 5.3 0.9 - - - -
230A PHE 3.7 1.2 - - - +
231A PHE* 3.4 10.1 - - - -
232A VAL* 2.9 42.6 + - + +
234A PHE* 3.8 19.9 - - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.5 0.9 - - + -
112A PHE* 3.7 29.4 - - + -
126A GLU* 1.3 72.4 - - - +
128A ARG* 1.3 63.1 + - - +
129A LEU* 3.7 25.7 + - + +
149A VAL* 4.1 13.9 - - + -
180A GLU 3.5 3.1 - - - +
182A LEU* 2.8 43.8 + - + +
184A VAL* 3.7 17.4 - - + +
203A LEU* 3.8 30.1 - - + -
205A VAL* 4.1 10.8 - - + -
229A PRO* 4.7 2.2 - - + -
230A PHE 4.0 7.4 - - - +
231A PHE* 3.9 9.4 - - + -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 3.3 51.0 + - - +
126A GLU* 4.5 8.0 + - + -
127A LEU* 1.3 72.7 - - - +
129A LEU* 1.3 62.2 + - - +
179A TRP* 3.4 47.8 + - + +
180A GLU 3.3 4.3 - - - +
181A THR* 2.8 33.2 + - - +
229A PRO* 3.4 19.2 - - - +
230A PHE* 3.2 50.2 + - + +
232A VAL* 4.0 7.9 - - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.0 9.2 - - + -
127A LEU* 3.9 20.6 - - + +
128A ARG* 1.3 76.8 - - - +
130A TYR* 1.3 61.2 + - - +
131A VAL 3.7 0.9 + - - -
147A MET* 4.0 15.3 - - + -
178A GLY 3.7 0.2 - - - +
179A TRP* 3.3 6.5 - - - -
180A GLU* 2.8 35.1 + - - +
182A LEU* 3.8 25.8 - - + -
205A VAL* 3.9 18.4 - - + -
219A ILE* 3.9 30.1 - - + -
229A PRO* 3.6 35.0 - - + -
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 1.3 70.7 - - - +
131A VAL* 1.3 61.6 + - - +
132A SER* 3.5 21.1 + - - -
177A GLU* 3.2 25.7 + - + +
178A GLY* 3.5 31.0 - - - -
179A TRP* 3.7 28.2 - + + -
219A ILE* 3.3 6.0 - - - +
220A SER* 3.1 46.8 + - - +
227A ASN* 3.4 50.6 + - + +
229A PRO* 5.9 0.2 - - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU 4.8 0.9 - - - +
130A TYR* 1.3 70.0 - - - +
132A SER* 1.3 67.0 + - - +
143A LEU* 3.9 11.9 - - + -
147A MET* 4.1 15.5 - - + -
174A ILE* 3.6 48.9 - - + -
176A ASP 4.2 9.2 - - - +
177A GLU* 3.3 4.5 - - - -
178A GLY 2.8 37.4 + - - +
180A GLU* 3.8 16.2 - - + -
217A LEU* 3.8 13.0 - - + -
218A ASP 3.8 4.7 - - - +
219A ILE* 4.1 7.9 - - + -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 3.5 25.4 + - - -
131A VAL* 1.3 77.9 - - - +
133A CYS* 1.3 68.5 + - - +
134A GLN* 3.0 23.2 + - - -
143A LEU* 4.2 5.2 - - - -
177A GLU* 2.8 24.2 + - - -
217A LEU* 4.5 2.2 - - - -
218A ASP 3.0 28.6 + - - +
220A SER* 4.6 0.4 - - - -
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Residues in contact with CYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 1.3 76.5 + - - +
134A GLN* 1.3 51.2 + - - +
135A ASN* 2.6 22.7 + - - +
136A ASP* 4.5 3.4 - - - -
139A SER* 3.8 32.3 - - - +
142A GLY 5.1 0.4 - - - +
143A LEU* 3.4 26.5 - - + +
177A GLU* 4.9 1.2 + - - -
214A CYS* 2.0 50.9 - - + -
216A THR* 3.6 5.6 - - - -
217A LEU* 4.6 2.0 - - - +
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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