Contacts of the strand formed by residues 210 - 221 (chain A) in PDB entry 6CU0
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 GLN 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LEU 3.6 1.2 - - - +
134A VAL* 3.5 1.6 - - - -
135A VAL* 2.9 34.9 + - + +
167A LEU* 3.9 30.3 - - + +
168A GLN 3.4 5.3 - - - +
169A PRO* 3.2 41.0 + - - +
171A ARG* 5.1 7.3 - - - +
205A HIS 4.9 1.4 + - - -
206A LEU* 4.4 8.4 - - + +
207A SER* 3.2 49.2 + - - +
208A ALA 3.3 1.6 - - - -
209A GLY* 1.3 77.0 - - - +
211A ARG* 1.3 60.3 + - - +
212A LEU* 3.9 16.6 - - + -
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Residues in contact with ARG 211 (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 THR* 4.3 13.1 + - - +
132A GLU* 2.8 48.1 + - + +
133A LEU 3.2 7.9 - - - +
134A VAL* 4.1 20.4 - - + -
166A HIS 3.9 0.2 - - - +
168A GLN* 2.9 69.7 + - - +
169A PRO* 5.2 3.2 - - - +
209A GLY 3.9 11.4 - - - +
210A GLN* 1.3 74.6 - - - +
212A LEU* 1.3 63.0 + - - +
213A GLY 3.9 1.0 + - - -
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Residues in contact with LEU 212 (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 GLU* 3.3 4.7 - - - -
133A LEU* 2.8 51.2 + - + +
135A VAL* 3.4 31.0 - - + -
143A VAL* 4.5 6.7 - - + -
165A LEU* 4.0 29.8 - - + -
166A HIS 3.7 5.4 - - - -
167A LEU* 3.7 17.0 - - + -
206A LEU* 4.2 12.3 - - + -
210A GLN* 3.8 16.6 - - + +
211A ARG* 1.3 72.1 - - - +
213A GLY* 1.3 58.0 + - - +
235A LEU* 5.2 5.4 - - + +
237A LEU* 3.8 26.0 - - + -
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Residues in contact with GLY 213 (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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109A TRP* 5.8 0.7 - - - -
131A LYS 4.2 12.8 - - - -
132A GLU* 4.7 7.1 + - - +
164A ALA 3.8 0.3 - - - +
165A LEU* 3.5 2.9 - - - -
166A HIS* 2.8 38.0 + - - +
211A ARG 3.9 1.0 + - - -
212A LEU* 1.3 74.3 - - - +
214A VAL* 1.3 65.8 + - - -
215A HIS* 4.2 9.8 + - - -
235A LEU* 6.0 0.2 - - - -
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Residues in contact with VAL 214 (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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106A PRO* 3.4 6.5 - - - +
107A LEU* 3.0 45.9 + - + +
109A TRP* 3.6 31.9 - - + +
131A LYS 4.9 1.8 + - - -
145A PHE* 4.1 12.3 - - + -
163A LEU* 4.1 24.5 - - + -
164A ALA 3.4 9.2 - - - +
165A LEU* 3.7 19.7 - - + -
213A GLY* 1.3 75.1 - - - -
215A HIS* 1.3 65.5 + - - +
235A LEU* 3.8 13.2 - - + -
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Residues in contact with HIS 215 (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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105A GLY* 4.4 3.8 - - - -
106A PRO* 3.7 38.6 - - + +
162A SER 3.5 4.7 - - - +
163A LEU* 3.5 2.4 - - - -
164A ALA* 2.8 38.9 + - + +
166A HIS* 3.4 34.3 - + + +
213A GLY* 4.2 12.7 + - - -
214A VAL* 1.3 78.6 - - - +
216A LEU* 1.3 61.8 + - - +
217A HIS* 4.0 1.0 + - - +
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Residues in contact with LEU 216 (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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99A ASN* 5.9 0.4 - - + -
101A LEU 4.5 3.8 - - - +
102A LEU* 4.1 18.4 - - + -
103A ILE 3.8 29.4 - - - +
104A ASP* 3.4 3.9 - - - +
105A GLY 3.1 37.6 + - - +
106A PRO* 4.7 0.2 - - - +
107A LEU* 3.8 23.6 - - + +
147A LEU* 5.1 0.2 - - + -
161A VAL* 3.5 28.7 - - + -
162A SER 3.3 3.6 - - - +
163A LEU* 3.5 23.8 - - + -
214A VAL 4.3 0.8 - - - -
215A HIS* 1.3 71.9 - - - +
217A HIS* 1.3 64.6 + - - +
218A THR* 4.8 2.5 - - + -
228A LEU* 4.6 13.2 - - + -
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Residues in contact with HIS 217 (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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104A ASP* 3.4 27.1 + - - +
161A VAL* 3.4 2.4 - - - +
162A SER* 2.7 53.7 + - - +
215A HIS 4.0 1.1 + - - +
216A LEU* 1.3 74.6 - - - +
218A THR* 1.3 85.1 + - - +
219A GLU* 4.5 3.6 + - + -
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Residues in contact with THR 218 (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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102A LEU* 4.1 33.5 - - + +
103A ILE 4.6 0.9 - - - +
104A ASP* 2.9 29.6 + - - +
160A SER 3.4 11.7 + - - -
161A VAL* 4.2 14.4 - - - +
185A LEU* 5.8 1.0 - - - +
216A LEU* 4.8 5.4 - - + -
217A HIS* 1.3 87.8 + - - +
219A GLU* 1.3 58.4 + - - +
220A ALA* 3.2 20.3 + - + +
223A ARG* 4.4 10.5 - - + +
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Residues in contact with GLU 219 (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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158A SER 4.0 0.9 - - - +
159A GLY* 3.7 8.2 - - - -
160A SER* 3.0 41.5 + - - +
162A SER* 5.9 0.2 + - - -
185A LEU* 5.7 0.7 - - - +
217A HIS* 4.5 6.7 - - + +
218A THR* 1.3 67.9 + - - +
220A ALA* 1.3 62.9 + - - +
221A ARG* 3.5 2.6 + - - +
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Residues in contact with ALA 220 (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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158A SER 4.9 0.2 - - - -
218A THR* 3.2 14.5 + - - +
219A GLU* 1.3 70.1 - - - +
221A ARG* 1.3 60.2 + - - +
222A ALA 3.8 1.3 - - - +
223A ARG* 3.6 31.0 - - + +
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Residues in contact with ARG 221 (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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157A GLY* 3.5 1.0 - - - -
158A SER* 3.1 53.3 + - - +
159A GLY* 5.2 1.3 - - - -
219A GLU 3.5 1.2 + - - +
220A ALA* 1.3 72.0 - - - +
222A ALA* 1.3 65.7 - - - +
223A ARG 4.2 0.8 - - - +
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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