Contacts of the strand formed by residues 135 - 145 (chain A) in PDB entry 3Q3G
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLN* 3.2 38.9 + - - +
131A LEU* 3.4 9.9 + - - +
133A SER* 3.4 5.3 - - - -
134A GLY* 1.3 79.7 - - - +
136A ALA* 1.3 60.8 + - - +
186A THR* 6.1 1.1 - - - -
187A LEU 4.3 5.8 - - - -
188A THR* 4.6 0.2 - - - -
189A LYS 4.3 0.9 - - - -
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Residues in contact with ALA 136 (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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126A PRO* 3.8 14.6 - - + -
130A GLN* 3.9 2.2 - - - +
131A LEU* 3.9 8.5 - - + -
135A GLY* 1.3 74.0 - - - +
137A SER* 1.3 60.8 + - - +
185A LEU 3.6 3.3 - - - +
186A THR* 4.5 0.6 - - - +
187A LEU* 3.0 38.1 + - - +
188A THR 3.6 8.3 - - - +
192A TYR* 3.5 38.1 - - + -
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Residues in contact with SER 137 (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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125A PRO 4.3 0.7 - - - +
126A PRO* 3.4 21.0 - - - +
130A GLN* 3.0 30.6 + - - +
136A ALA* 1.3 71.4 - - - +
138A VAL* 1.3 61.3 + - - +
139A VAL* 4.1 4.6 + - - +
184A THR* 3.8 10.5 - - - +
185A LEU 3.4 5.2 - - - -
186A THR* 2.8 28.1 + - - +
135B LEU* 5.3 1.9 - - - +
152B LEU* 3.8 18.3 - - - +
154B LYS* 3.6 8.1 - - - +
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Residues in contact with VAL 138 (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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123A ILE* 4.2 2.5 - - + -
124A PHE 3.4 17.0 - - - +
126A PRO* 4.0 18.8 - - + -
137A SER* 1.3 75.5 - - - +
139A VAL* 1.3 58.7 + - - +
154A TRP* 3.7 30.5 - - + -
184A THR* 3.2 5.0 - - - -
185A LEU* 2.7 49.0 + - + +
187A LEU* 4.3 14.1 - - + -
192A TYR* 4.3 11.9 - - + -
198A TYR* 4.5 10.1 - - + -
215A PHE* 3.5 21.8 - - + -
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Residues in contact with VAL 139 (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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123A ILE* 3.4 5.9 - - - +
124A PHE* 2.8 43.0 + - + +
137A SER 4.6 2.2 - - - +
138A VAL* 1.3 77.5 - - - +
140A CYS* 1.3 65.0 + - - +
141A PHE* 3.7 35.9 - - + -
154A TRP* 4.2 1.3 - - - -
182A SER* 4.3 2.2 - - - +
183A SER 3.5 6.3 - - - +
184A THR* 3.9 22.9 - - + +
135B LEU* 3.8 34.5 - - + -
152B LEU* 4.4 14.8 - - + -
189B SER* 4.9 1.8 - - - +
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Residues in contact with CYS 140 (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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121A VAL* 3.8 7.2 - - - -
122A SER 3.2 5.4 - - - -
139A VAL* 1.3 74.6 - - - +
141A PHE* 1.3 62.1 + - - +
142A LEU* 3.6 26.0 - - - +
152A VAL* 4.9 2.7 - - - -
154A TRP* 3.6 17.0 - - + -
181A MET 3.9 0.5 - - - +
182A SER* 3.6 2.8 + - - -
183A SER* 2.8 42.4 + - - +
200A CYS* 2.0 47.3 - - + -
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Residues in contact with PHE 141 (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 THR 3.3 1.6 - - - +
121A VAL* 3.2 6.6 - - - -
122A SER* 2.9 35.9 + - - +
124A PHE* 3.4 27.8 - + - -
139A VAL* 3.7 14.6 - - + -
140A CYS* 1.3 73.1 - - - +
142A LEU* 1.3 61.9 + - - +
143A ASN* 3.8 17.0 - - - +
181A MET 3.5 2.5 - - - -
182A SER* 3.6 11.9 - - - -
135B LEU* 4.1 8.3 - - + -
148B THR* 4.0 6.7 - - + -
149B LEU 4.2 0.9 - - - -
150B GLY* 4.0 8.5 - - - -
177B PHE* 3.4 26.7 - + - -
189B SER* 3.6 17.7 - - - -
190B SER 3.5 22.0 - - - -
191B SER* 3.5 27.6 - - - -
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Residues in contact with LEU 142 (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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119A PRO* 4.1 14.1 - - + -
120A THR 3.7 3.8 - - - -
121A VAL* 3.7 16.4 - - + -
140A CYS* 3.6 25.1 - - - -
141A PHE* 1.3 77.1 - - - +
143A ASN* 1.3 58.2 + - - +
145A PHE* 3.4 12.5 - - + -
150A ILE* 3.9 21.3 - - + -
151A ASN 4.7 0.2 - - - +
152A VAL* 3.5 25.4 - - + -
180A SER* 3.3 3.1 - - - -
181A MET* 2.7 60.0 + - + +
201A GLU 6.1 0.2 - - - -
202A ALA* 3.8 17.9 - - + -
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Residues in contact with ASN 143 (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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119A PRO* 3.5 1.2 - - - +
120A THR* 2.9 44.1 + - - +
122A SER* 5.9 0.2 + - - -
141A PHE* 3.8 13.3 - - - +
142A LEU* 1.3 76.9 - - - +
144A ASN* 1.3 80.1 - - - +
145A PHE* 3.5 2.7 - - - -
180A SER* 3.4 5.9 - - - +
148B THR* 4.5 8.1 + - - +
175B HIS* 3.6 12.7 + - - -
177B PHE* 3.3 28.4 - - - -
191B SER* 2.9 27.1 + - - -
193B THR* 4.8 5.5 + - - -
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Residues in contact with ASN 144 (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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117A ALA* 3.7 10.7 - - - +
118A ALA 3.6 10.2 - - - +
120A THR* 5.2 4.6 + - - +
143A ASN* 1.3 79.7 - - - +
145A PHE* 1.3 59.4 + - - +
173A ASP* 5.6 1.4 - - - -
176A ASP* 3.1 26.6 + - - +
178A THR* 3.4 20.8 + - + +
179A TYR 3.2 5.3 + - - -
180A SER* 3.0 9.1 + - - -
175B HIS* 2.9 36.8 + - - -
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Residues in contact with PHE 145 (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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117A ALA* 3.4 15.9 - - - +
119A PRO* 3.6 24.9 - - + -
142A LEU* 3.4 26.5 - - + -
144A ASN* 1.3 75.3 - - - +
146A TYR* 1.4 59.7 + - - +
147A PRO 3.3 15.3 - - - -
148A LYS 3.3 25.8 - - - -
150A ILE* 3.5 40.4 - - + -
169A TRP* 5.1 2.9 - + - -
178A THR* 3.4 4.7 - - - -
179A TYR* 2.7 67.6 + - + +
180A SER 4.5 0.9 - - - -
181A MET* 3.9 18.2 - - + -
204A HIS* 3.8 6.1 - - - +
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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