Contacts of the strand formed by residues 164 - 175 (chain D) in PDB entry 1D2H
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 VAL 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D GLY* 4.8 1.1 - - - -
130D PHE 4.0 0.4 - - - -
131D ASP 4.6 1.3 - - - +
133D VAL* 3.0 31.2 - - + -
160D ILE 4.1 5.8 - - - +
161D ALA* 3.0 19.9 + - - +
162D SER 3.2 3.9 - - - +
163D MET* 1.3 78.0 - - - +
165D ARG* 1.3 56.1 + - - +
168D GLY* 3.3 31.6 - - - -
169D LEU 3.4 18.2 - - - +
170D LEU* 4.6 9.0 - - + -
258D PHE* 4.7 2.2 - - + -
288D LEU 4.8 0.4 - - - +
290D LYS* 2.6 48.7 + - + -
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Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D HIS 5.4 4.8 + - - -
56D GLY 4.8 7.9 + - - -
57D CYS* 5.5 2.6 - - - -
128D ASP 3.5 20.4 - - - +
129D GLY* 3.7 10.7 - - - -
130D PHE 3.0 29.7 + - - +
131D ASP* 2.6 39.6 + - - +
164D VAL* 1.3 74.3 - - - +
166D PRO* 1.3 99.5 + - + +
167D GLY* 3.8 16.2 + - - -
168D GLY* 2.8 17.4 + - - -
290D LYS* 3.4 2.0 - - - +
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Residues in contact with PRO 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ASP 5.0 2.9 - - - +
164D VAL 4.5 0.9 - - - +
165D ARG* 1.3 128.2 + - + +
167D GLY* 1.3 57.2 + - - +
168D GLY 2.7 0.2 - - - -
290D LYS* 3.6 8.7 - - + +
292D GLY* 2.7 31.4 - - - +
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Residues in contact with GLY 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D HIS* 5.9 1.0 - - - +
57D CYS* 5.8 2.1 - - - -
131D ASP 4.9 0.2 - - - +
165D ARG* 3.8 16.4 + - - -
166D PRO* 1.3 73.6 - - - +
168D GLY* 1.3 63.3 + - - +
169D LEU* 5.1 1.0 - - - +
289D LYS* 4.1 24.8 - - - +
290D LYS 2.7 12.8 + - - -
291D THR* 4.3 8.1 - - - +
292D GLY 4.6 0.2 - - - +
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Residues in contact with GLY 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ASP 3.8 10.1 - - - -
164D VAL* 3.3 11.2 - - - -
165D ARG* 2.8 17.8 + - - -
166D PRO 2.7 4.6 + - - -
167D GLY* 1.3 80.5 - - - +
169D LEU* 1.3 59.4 + - - +
288D LEU 3.4 2.7 - - - -
289D LYS* 2.6 34.5 - - - -
290D LYS 3.1 6.1 + - - -
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 3.4 15.7 - - + +
52D LEU* 4.9 7.9 - - + -
55D HIS* 2.9 64.2 - - + +
57D CYS* 4.3 11.4 - - - -
131D ASP 3.3 11.6 + - - +
132D ALA* 3.7 5.1 - - + -
133D VAL* 3.0 32.8 + - - +
164D VAL* 3.4 4.4 - - - +
167D GLY 5.1 1.1 - - - +
168D GLY* 1.3 82.0 - - - +
170D LEU* 1.3 60.9 + - - +
171D VAL* 5.2 6.3 - - + -
287D VAL* 4.2 12.3 - - + -
288D LEU 2.7 7.2 - - - +
289D LYS* 3.8 16.2 - - + +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D VAL* 3.3 14.4 - - + +
135D CYS* 4.9 2.7 - - + -
157D LEU* 5.5 2.5 - - + +
160D ILE* 4.3 27.4 - - + -
161D ALA* 4.8 7.0 - - + -
164D VAL* 4.6 3.8 - - + -
169D LEU* 1.3 75.5 - - - +
171D VAL* 1.3 69.0 + - - +
172D ILE* 3.7 24.5 - - + +
254D VAL* 4.3 13.9 - - + +
258D PHE* 3.7 26.2 - - + -
286D HIS 2.8 1.9 - - - +
287D VAL* 2.7 36.2 - - - -
288D LEU* 2.9 32.8 + - + +
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Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D TRP* 3.8 24.7 - - + -
48D LEU* 5.1 5.8 - - + -
51D LEU* 5.4 6.1 - - + -
52D LEU* 5.2 8.3 - - + -
133D VAL 3.1 6.3 + - - +
134D ILE* 4.1 15.7 - - + -
135D CYS 2.9 18.1 + - - -
136D LEU* 2.6 66.6 - - + +
169D LEU* 5.2 7.9 - - + -
170D LEU* 1.3 86.9 - - - +
172D ILE* 1.3 54.6 + - - +
285D ILE* 3.8 8.1 - - + -
286D HIS 3.4 2.9 - - - -
287D VAL* 5.0 7.9 - - + -
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Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D CYS* 3.4 30.1 - - + -
136D LEU* 4.3 0.2 - - - -
140D PHE* 4.1 15.0 - - + -
157D LEU* 2.8 39.9 - - + -
160D ILE* 5.1 3.6 - - + -
170D LEU* 3.7 15.0 - - + +
171D VAL* 1.3 74.4 - - - +
173D ASP* 1.3 59.3 + - - +
250D PHE* 2.9 41.1 - - + -
254D VAL* 4.4 6.7 - - + -
286D HIS* 3.0 36.4 + - + +
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Residues in contact with ASP 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D CYS 3.2 11.4 + - - +
136D LEU* 3.8 7.7 - - + -
137D GLY 2.7 14.1 + - - -
138D ASN* 2.6 26.1 + - - -
140D PHE* 4.7 10.0 + - - +
171D VAL 3.8 0.6 + - - -
172D ILE* 1.3 75.6 - - - +
174D HIS* 1.3 69.5 + - - +
193D TYR* 2.6 46.3 + - - +
250D PHE* 4.4 5.7 - - - -
283D TYR* 3.7 5.9 - - + -
284D PHE 3.3 13.0 - - - +
285D ILE* 4.4 8.3 - - + -
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Residues in contact with HIS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ASN* 4.0 8.7 - - - +
140D PHE* 6.0 0.2 - - + -
141D ALA* 5.0 7.9 - - + +
173D ASP* 1.3 87.4 + - - +
175D LYS* 1.3 74.2 + - - +
177D TYR* 5.2 0.4 - - + -
245D HIS* 4.0 22.3 + - + +
247D LEU* 4.2 8.0 + - - -
250D PHE* 3.2 45.5 - - + -
283D TYR* 3.6 4.7 - - - -
284D PHE* 3.0 54.6 + + + +
286D HIS* 3.4 19.7 - - - -
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Residues in contact with LYS 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ASN* 3.2 16.3 + - - +
174D HIS* 1.3 87.4 + - - +
176D ASN* 1.3 54.7 + - - +
177D TYR* 2.7 61.1 + - + +
180D ILE* 4.7 10.8 - - + -
187D PRO* 5.6 8.5 + - - -
190D LYS 4.0 3.2 + - - -
191D ASN* 5.0 1.4 - - - +
245D HIS 3.8 0.5 - - - +
282D CYS* 2.6 47.3 - - - +
283D TYR* 2.6 45.4 + - + +
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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