Contacts of the strand formed by residues 138 - 145 (chain A) in PDB entry 6DXW
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 ILE 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 4.0 16.6 - - + -
131A ALA 3.4 4.9 - - - +
132A GLN* 4.0 24.5 - - + +
136A GLY 4.1 2.9 - - - +
137A HIS* 1.3 79.0 - - - +
139A TYR* 1.3 68.2 + - - +
140A HIS* 5.5 1.1 - - + -
190A THR* 5.6 0.4 - - - +
251A GLY* 4.0 3.4 - - - -
252A GLY 3.6 26.0 - - - +
253A THR* 4.7 2.8 + - - +
254A SER 3.5 26.5 - - - +
256A ARG 4.1 1.8 - - - +
257A GLU 3.7 31.0 - - - +
274A LEU* 4.1 6.7 - - + -
342A SER* 2.7 31.1 + - - -
343A ALA 5.1 0.2 + - - -
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Residues in contact with TYR 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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129A ILE 4.0 0.2 - - - +
130A VAL* 3.4 6.4 - - - +
131A ALA 2.8 33.8 + - - +
133A ASP* 2.8 33.6 + - + -
137A HIS* 3.4 34.4 + - + +
138A ILE* 1.3 76.6 - - - +
140A HIS* 1.3 62.9 + - - +
316A LEU* 3.5 31.2 + - + -
317A SER* 3.8 14.9 - - - -
318A LEU* 3.7 32.8 - - + -
321A LEU* 3.8 18.1 - - + +
341A MET 4.1 3.4 - - - -
342A SER* 4.9 4.7 - - - -
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Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 4.8 0.2 - - - -
129A ILE 3.3 13.2 - - - -
130A VAL* 4.8 4.9 - - + +
138A ILE* 5.5 0.9 - - + -
139A TYR* 1.3 78.1 - - - +
141A GLY* 1.3 76.9 + - - +
190A THR* 2.8 33.2 + - - +
192A SER* 3.1 30.3 + - - -
249A ILE* 3.2 40.8 - - + +
250A VAL 4.4 0.2 - - - -
251A GLY* 3.8 6.3 + - - -
318A LEU* 4.2 0.4 - - - +
321A LEU* 3.6 6.2 - - - +
340A VAL* 3.4 1.9 - - - -
341A MET* 2.7 61.4 + - + +
342A SER* 5.4 0.7 - - - -
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Residues in contact with GLY 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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128A SER* 3.5 0.3 - - - -
129A ILE* 2.7 41.4 + - - +
140A HIS* 1.3 79.8 - - - +
142A ARG* 1.3 62.4 + - - +
321A LEU* 3.6 9.8 - - - +
325A LEU* 3.7 16.6 - - - -
339A THR 3.1 10.3 - - - -
340A VAL* 4.2 2.2 - - - -
341A MET* 5.5 0.4 - - - -
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Residues in contact with ARG 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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126A ALA* 3.3 20.0 - - - +
127A THR 3.0 12.6 - - - +
128A SER* 3.6 13.9 - - - +
140A HIS* 5.2 0.2 - - - +
141A GLY* 1.3 75.9 - - - +
143A ASN* 1.3 90.2 + - - +
144A LEU* 4.3 9.7 - - - +
181A TRP* 2.7 37.4 + - - +
182A THR* 2.5 35.8 + - + +
192A SER* 3.9 10.1 - - - -
193A GLY 2.8 21.2 + - - +
194A ASP* 3.6 4.6 + - - -
325A LEU* 3.4 6.6 - - - +
337A TYR* 3.9 15.5 + - - -
338A THR* 3.4 1.2 - - - +
339A THR* 2.9 37.4 + - - +
341A MET* 5.1 2.2 - - + -
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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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126A ALA* 3.2 1.6 - - - -
127A THR* 2.7 32.0 + - - +
142A ARG* 1.3 92.2 + - - +
144A LEU* 1.3 59.5 + - - +
145A ASP* 4.0 11.7 - - - +
325A LEU* 2.7 35.9 + - + +
330A VAL* 3.1 27.7 + - - +
331A TYR* 3.9 4.4 - - - +
335A THR* 4.0 8.6 - - + +
337A TYR 3.6 2.5 - - - -
338A THR* 2.6 36.8 + - - +
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Residues in contact with LEU 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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124A VAL* 3.7 29.8 - - + -
125A PHE 3.6 2.7 - - - +
142A ARG* 4.3 10.8 - - - +
143A ASN* 1.3 73.6 - - - +
145A ASP* 1.3 62.0 + - - +
146A TYR* 5.0 3.1 - - + -
152A LEU* 5.5 0.4 - - + -
174A PHE* 3.9 25.1 - - + -
181A TRP* 4.0 24.2 - - + -
335A THR* 3.6 0.2 - - - -
336A ILE* 2.6 50.3 + - + +
337A TYR* 3.1 46.8 + - + +
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Residues in contact with ASP 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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124A VAL* 3.6 8.5 - - - +
125A PHE* 2.7 52.1 + - + +
126A ALA* 4.5 1.3 + - - -
127A THR* 5.3 0.2 + - - -
143A ASN* 4.0 5.4 - - - +
144A LEU* 1.3 86.4 + - - +
146A TYR* 1.3 61.1 + - - +
147A PRO* 4.3 1.1 - - - +
300A ARG* 4.1 17.0 + - - -
330A VAL 4.3 2.8 - - - +
332A ASN* 2.9 29.5 + - - +
334A PHE* 3.2 18.4 - - + +
335A THR* 3.1 21.8 + - - +
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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