Contacts of the strand formed by residues 240 - 248 (chain A) in PDB entry 4TZQ
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 HIS 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.7 10.1 - - + -
38A SER* 2.5 31.6 + - - +
39A SER* 3.6 23.4 + - - -
42A MET* 3.8 22.0 - - + -
100A THR* 2.8 31.4 + - - -
101A LYS* 4.7 4.0 + - - -
129A PHE* 6.1 2.0 - + + -
130A ILE 4.0 5.2 - - - +
131A TYR* 3.4 32.7 - + - -
132A PHE* 4.0 7.0 - - - -
236A ARG* 3.3 14.9 - - - -
237A PRO* 3.2 20.6 + - + +
238A GLY 3.8 0.2 - - - -
239A CYS* 1.3 91.2 + - + +
241A ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 241 (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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42A MET* 5.1 1.3 - - - -
129A PHE* 3.3 5.9 - - - +
130A ILE* 2.9 52.3 + - + +
132A PHE* 3.8 8.7 - - + -
156A LEU* 3.9 20.0 - - + +
159A LEU* 5.1 0.9 - - + -
235A LEU 3.3 9.9 - - - +
236A ARG* 3.9 8.7 - - + -
237A PRO* 4.8 0.2 - - - -
240A HIS* 1.3 78.6 - - - +
242A ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 242 (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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42A MET* 3.6 28.0 - - + -
127A MET* 4.6 9.4 - - + -
128A LYS 3.1 14.1 - - - +
129A PHE* 3.6 12.6 - - + -
156A LEU* 3.5 7.3 - - - +
234A HIS* 3.2 8.2 - - - +
235A LEU* 2.9 35.6 + - + +
241A ALA* 1.3 77.3 - - - +
243A ASN* 1.3 60.7 + - - +
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Residues in contact with ASN 243 (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 SER 3.5 1.9 - - - +
127A MET* 3.4 3.8 - - - -
128A LYS* 2.9 34.4 + - + +
152A HIS* 5.2 11.1 - - + +
155A LYS* 3.2 33.6 + - - +
156A LEU* 3.9 17.5 - - + -
231A THR* 4.1 4.6 + - - +
233A GLY 3.2 17.6 - - - +
234A HIS* 3.9 0.9 - - - +
242A ALA* 1.3 76.0 - - - +
244A MET* 1.3 63.3 + - - +
245A GLU* 3.4 36.3 + - - +
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Residues in contact with MET 244 (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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49A ALA* 3.8 30.3 - - + +
50A PHE* 4.5 11.7 - - + -
53A VAL* 3.7 29.8 - - + -
125A PHE* 4.5 6.3 - - + -
126A SER 3.1 10.1 - - - +
127A MET* 3.8 26.2 - - + +
174A ILE* 4.1 19.1 - - + -
178A VAL* 4.6 1.3 - - + -
232A ILE* 2.9 46.8 + - + +
233A GLY 2.8 20.5 + - - +
243A ASN* 1.3 74.3 + - - +
245A GLU* 1.3 68.5 + - - +
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Residues in contact with GLU 245 (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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124A VAL 3.7 0.5 - - - +
125A PHE* 3.5 3.8 - - - -
126A SER* 2.9 35.6 + - - +
128A LYS* 4.4 17.7 + - - +
152A HIS* 5.6 1.9 - - - +
229A SER* 5.8 2.2 - - - -
230A ALA 3.7 6.3 - - - +
231A THR* 4.3 19.5 + - - +
232A ILE* 4.1 6.4 - - - +
243A ASN* 3.4 28.1 + - - +
244A MET* 1.3 80.1 - - - +
246A CYS* 1.3 62.1 + - - +
247A TRP* 3.7 36.5 + - + +
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Residues in contact with CYS 246 (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 GLU* 4.9 0.7 - - - -
124A VAL 3.5 5.2 - - - -
125A PHE* 3.7 34.1 - - + -
181A LEU* 3.6 25.6 - - + -
186A LEU* 4.1 18.2 - - - -
229A SER* 3.1 7.3 - - - -
230A ALA 2.9 33.6 + - - +
232A ILE* 4.0 1.3 - - + +
245A GLU* 1.3 73.0 - - - +
247A TRP* 1.3 65.0 + - - +
248A SER* 4.4 4.7 - - - -
251A MET* 3.5 17.5 - - + +
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Residues in contact with TRP 247 (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 GLU* 3.2 4.2 - - - +
124A VAL* 2.7 60.1 + - + +
126A SER* 3.2 27.2 + - - -
128A LYS* 4.8 12.5 - - - +
221A TYR* 5.0 4.1 + - - -
223A LEU* 3.6 36.1 - - + -
227A ILE* 4.0 18.6 - - + -
228A GLN 3.4 9.2 - - - -
229A SER* 3.6 28.5 - - - -
245A GLU* 3.7 32.1 + - + +
246A CYS* 1.3 74.1 - - - +
248A SER* 1.3 62.0 + - - +
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Residues in contact with SER 248 (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 3.7 3.8 - - - -
123A GLU* 2.8 30.0 + - - +
186A LEU* 3.5 19.4 - - - +
227A ILE* 3.4 10.3 - - - +
228A GLN* 3.0 40.1 + - - +
246A CYS* 4.1 1.5 - - - -
247A TRP* 1.3 77.4 - - - +
249A MET* 1.3 60.9 + - - +
250A LEU* 3.0 15.8 + - - +
251A MET* 4.0 10.6 - - - +
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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