Contacts of the strand formed by residues 163 - 175 (chain A) in PDB entry 4JDA
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 ARG 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASP* 4.2 17.7 - - - -
154A VAL* 3.8 2.6 - - - -
155A VAL* 3.2 49.0 + - + +
161A LYS 3.6 5.0 + - - +
162A LYS* 1.3 74.4 - - - +
164A VAL* 1.3 62.5 + - - +
165A TYR* 3.8 32.0 + - - -
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Residues in contact with VAL 164 (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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59A ASP* 4.2 5.2 - - - +
60A ALA* 4.0 9.4 + - - -
61A PRO* 3.9 37.2 - - + -
152A GLU* 4.3 12.6 - - + +
153A PHE 3.4 9.4 - - - +
154A VAL* 4.2 18.6 - - + -
162A LYS* 4.6 6.1 - - + +
163A ARG* 1.3 81.9 - - - +
165A TYR* 1.3 61.0 + - - +
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Residues in contact with TYR 165 (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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29A GLU* 2.6 39.5 + - - +
57A ARG* 3.9 17.9 - - + -
58A VAL 3.5 13.2 - - - +
59A ASP* 3.9 16.2 - - - +
60A ALA 3.9 3.1 - - - -
152A GLU* 3.6 2.4 - - - +
153A PHE* 2.8 54.1 + - + +
155A VAL* 4.1 24.3 - - + +
163A ARG* 3.8 25.1 - - - -
164A VAL* 1.3 75.2 - - - +
166A SER* 1.3 74.0 + - - +
167A VAL* 3.8 15.5 - - + -
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Residues in contact with SER 166 (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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57A ARG* 3.3 4.7 - - - -
58A VAL* 2.9 29.3 + - - +
60A ALA 2.6 23.4 + - - -
61A PRO 3.5 0.2 - - - -
62A ALA* 3.2 22.2 + - - +
65A ILE* 3.8 18.6 - - - -
150A VAL* 4.1 12.3 - - - -
151A ASN 3.2 10.8 - - - -
152A GLU* 4.2 1.7 - - - -
165A TYR* 1.3 79.7 + - - +
167A VAL* 1.3 65.2 + - - +
168A VAL 4.0 0.4 - - - -
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Residues in contact with VAL 167 (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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25A LEU* 4.4 10.8 - - + -
29A GLU* 4.3 11.2 - - + +
33A LEU* 3.9 12.6 - - + -
55A ALA* 4.6 2.9 - - + -
56A HIS 3.7 6.5 - - - +
57A ARG* 4.2 11.2 - - + -
151A ASN* 2.8 36.4 + - - -
153A PHE* 3.5 27.4 - - + -
165A TYR* 3.8 16.2 - - + -
166A SER* 1.3 76.1 - - - +
168A VAL* 1.3 66.2 + - - +
169A LEU* 3.6 27.4 - - + -
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Residues in contact with VAL 168 (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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54A ILE 3.9 0.5 - - - +
55A ALA* 3.4 3.8 - - - -
56A HIS* 2.8 42.6 + - + +
58A VAL* 4.1 9.2 - - + -
65A ILE* 4.0 37.7 - - + -
69A VAL* 5.3 0.2 - - + -
148A THR* 4.0 20.6 - - + -
149A SER 3.4 6.7 - - - +
150A VAL* 4.6 8.7 - - + -
167A VAL* 1.3 74.7 - - - +
169A LEU* 1.3 61.7 + - - +
170A GLU 4.1 0.2 + - - -
197A LEU* 3.6 30.7 - - + +
200A LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 169 (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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25A LEU* 4.9 4.9 - - + -
33A LEU* 4.2 16.6 - - + -
36A ILE* 4.9 3.6 - - + -
37A ILE* 3.8 20.6 - - + -
41A HIS* 3.3 36.7 - - + +
53A LEU* 4.5 11.9 - - + -
54A ILE 3.6 3.8 - - - +
55A ALA* 3.8 18.4 - - + -
148A THR* 3.1 5.5 - - - +
149A SER* 2.9 39.7 + - - +
151A ASN* 4.1 13.9 - - - +
167A VAL* 3.6 25.6 - - + -
168A VAL* 1.3 75.4 - - - +
170A GLU* 1.3 59.8 + - - +
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.6 2.1 - - - -
54A ILE* 2.8 40.0 + - - +
78A TYR* 5.2 7.6 + - - -
79A LYS* 5.7 1.4 - - - -
132A PHE* 6.2 0.9 - - - -
144A TYR* 4.6 1.8 + - - +
146A SER* 4.6 10.1 - - - -
147A VAL 3.4 3.8 - - - +
148A THR* 2.7 35.0 + - + +
168A VAL 4.1 1.0 + - - -
169A LEU* 1.3 73.5 - - - +
171A SER* 1.3 63.8 + - - +
172A TYR* 5.2 2.8 - - - -
193A VAL* 3.6 33.0 - - + +
196A ASN* 4.7 8.2 - - - +
197A LEU* 4.4 25.9 - - + +
301A A9S 4.1 16.2 - - - +
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Residues in contact with SER 171 (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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41A HIS* 2.9 51.0 + - - -
43A PHE* 3.6 5.3 - - - -
52A SER 3.2 13.7 - - - -
53A LEU* 4.1 11.7 - - - -
146A SER* 3.1 6.5 - - - -
147A VAL* 2.9 30.2 + - - +
170A GLU* 1.3 75.8 - - - +
172A TYR* 1.3 65.3 + - - +
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Residues in contact with TYR 172 (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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43A PHE* 3.5 6.9 - - - -
50A CYS* 4.1 13.5 - - - -
51A THR* 2.8 26.3 + - - -
52A SER* 3.0 32.1 + - - -
54A ILE* 5.4 2.7 - - + -
144A TYR* 3.6 29.6 - + + +
145A ARG 3.2 12.3 - - - +
146A SER* 4.0 0.2 - - - -
170A GLU* 5.2 1.6 - - + -
171A SER* 1.3 81.1 - - - +
173A ILE* 1.3 68.3 + - - +
174A VAL* 4.4 8.5 - - + -
186A ARG* 3.5 13.2 + - - -
189A VAL* 3.3 38.2 - - + +
190A ASP* 2.7 30.3 + - - -
193A VAL* 4.4 12.3 - - + -
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Residues in contact with ILE 173 (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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43A PHE* 3.3 39.9 - - + -
44A PRO* 3.9 22.2 - - + +
45A ARG* 5.6 0.7 - - - -
46A SER* 4.3 3.8 - - - +
49A THR* 3.8 31.0 - - + +
50A CYS 3.3 11.7 - - - +
51A THR* 4.4 4.3 - - - +
143A ASN 3.4 5.6 - - - +
144A TYR* 3.4 1.7 - - - -
145A ARG* 2.8 66.8 + - + +
172A TYR* 1.3 77.2 - - - +
174A VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 174 (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 THR* 3.3 5.8 - - - -
50A CYS* 2.8 54.2 + - + +
141A LEU* 3.6 41.3 - - + +
142A ASN 3.6 11.0 - - - +
143A ASN 4.2 4.0 - - - -
144A TYR* 4.0 15.7 - - + -
172A TYR* 4.4 10.3 - - + -
173A ILE* 1.3 76.8 - - - +
175A ASP* 1.3 76.9 + - - +
185A THR* 5.0 6.1 - - - -
189A VAL* 5.4 4.0 - - + -
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Residues in contact with ASP 175 (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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48A ASN 3.7 7.0 - - - +
49A THR* 4.0 13.5 - - - +
140A ARG 5.1 0.2 - - - +
141A LEU* 4.9 2.1 - - - +
142A ASN* 3.1 37.6 + - + +
143A ASN* 3.4 30.9 + - - +
174A VAL* 1.3 88.9 - - - +
176A ILE* 1.3 62.9 + - - +
177A PRO* 3.3 12.5 - - + +
185A THR* 5.3 0.3 - - - -
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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