Contacts of the strand formed by residues 129 - 139 (chain B) in PDB entry 2HU4
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 CYS 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.8 20.0 - - + +
122B ILE* 4.6 1.6 - - + -
123B SER 3.9 1.1 - - - +
124B CYS* 2.1 47.3 - - - -
128B GLU* 1.3 79.4 - - - +
130B ARG* 1.3 64.3 + - - +
162B PRO* 4.0 4.9 - - - +
163B VAL* 3.3 41.1 + - + +
412B LEU* 4.4 17.7 - - - -
210D ILE* 5.5 2.9 - - - -
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE 4.0 0.2 - - - +
122B ILE* 3.4 8.3 - - - +
123B SER 3.1 31.1 + - - +
128B GLU* 3.7 32.4 + - + +
129B CYS* 1.3 77.9 - - - +
131B THR* 1.3 65.6 + - - +
132B PHE* 4.0 17.0 - - + -
160B SER* 2.8 47.8 + - - -
161B CYS* 3.4 11.3 - - - +
162B PRO* 3.7 21.6 - - - +
163B VAL* 3.8 1.6 - - - -
170B ASN 5.1 1.2 + - - -
172B ARG* 3.5 35.8 - - - +
189B TRP* 4.0 26.0 - - + +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASP* 5.3 3.8 - - - +
120B PRO* 4.8 7.6 - - + -
121B PHE 3.6 12.3 - - - +
122B ILE* 4.2 6.7 - - + +
130B ARG* 1.3 73.2 - - - +
132B PHE* 1.3 70.3 + - - +
133B PHE* 3.6 14.0 - - + -
160B SER* 3.0 22.7 - - - -
161B CYS* 2.8 26.4 + - - -
162B PRO 4.0 0.6 + - - -
163B VAL* 3.3 30.0 - - - +
164B GLY 4.2 2.6 + - - -
165B GLU 5.6 1.7 + - - +
167B PRO* 6.5 0.9 - - + -
443B SER* 4.9 13.7 - - - +
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Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PRO* 3.3 2.3 - - - +
121B PHE* 2.8 70.0 + + + -
123B SER* 4.2 7.0 - - - -
130B ARG* 4.0 18.4 - - + -
131B THR* 1.3 78.6 - - - +
133B PHE* 1.3 66.0 + - - +
158B LEU* 3.9 17.7 - - + -
159B MET 3.3 4.5 - - - -
160B SER* 3.7 13.5 - - - -
172B ARG* 5.7 0.2 - - - -
174B GLU* 3.7 28.9 - - + -
182B ALA* 4.0 17.0 - - + -
189B TRP* 3.7 48.7 - + - -
191B THR* 4.0 4.9 - - + -
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 4.4 2.5 - + - -
117B ILE* 3.9 30.3 - - + -
118B ARG 4.4 0.9 - - - +
119B GLU 3.9 9.4 - - - -
120B PRO* 4.2 5.2 - - + -
121B PHE* 5.5 0.2 - - - -
131B THR* 3.6 24.9 - - + -
132B PHE* 1.3 80.8 - - - +
134B LEU* 1.3 62.3 + - - +
135B THR* 3.6 23.6 - - + -
158B LEU* 3.3 8.7 - - - +
159B MET* 3.0 57.5 + - + -
160B SER* 3.8 2.0 - - - -
161B CYS* 3.8 12.3 - - - -
167B PRO* 3.4 25.8 - - + -
171B SER* 3.3 24.2 - - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 3.4 2.8 - - - -
118B ARG 3.3 25.0 + - - +
119B GLU* 3.7 24.5 - - + +
121B PHE* 6.3 1.1 - - + -
133B PHE* 1.3 74.6 - - - +
135B THR* 1.3 60.2 + - - +
156B ARG* 3.2 27.9 + - + +
157B THR 3.3 2.5 - - - +
158B LEU* 4.0 25.4 - - + -
177B ALA 3.6 20.4 - - - +
178B TRP 3.5 28.7 - - - +
179B SER* 3.6 8.1 - - - +
180B ALA* 4.1 15.9 - - + -
227B GLU* 3.8 10.5 - - - +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 3.8 29.0 - - + -
116B VAL 3.5 9.6 - - - -
117B ILE* 4.1 0.9 - - - -
133B PHE* 3.6 31.2 - - + -
134B LEU* 1.3 73.3 - - - +
136B GLN* 1.3 60.7 + - - +
137B GLY* 3.3 12.2 + - - -
156B ARG* 2.9 31.0 + - - +
157B THR* 2.7 36.8 + - - +
159B MET* 4.2 10.7 - - + -
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 3.0 36.9 + - + +
117B ILE* 5.1 1.3 - - - -
118B ARG* 5.4 2.8 - - - +
135B THR* 1.3 74.4 - - - +
137B GLY* 1.3 53.8 + - - +
138B ALA* 3.1 1.0 + - + +
148B THR* 3.5 49.3 + - + +
150B LYS* 4.5 9.8 - - - +
151B ASP* 4.7 9.1 + - - +
153B SER* 4.3 8.7 + - - -
155B HIS* 4.2 8.3 - - - +
156B ARG* 2.8 45.3 + - - +
107C ARG* 2.6 32.9 + - - -
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PHE* 5.3 3.6 - - - -
135B THR* 3.3 13.4 + - - -
136B GLN* 1.3 78.4 - - - +
138B ALA* 1.3 54.7 + - - +
155B HIS 3.8 4.1 + - - -
104C ASN* 3.4 30.3 - - - +
107C ARG* 2.8 35.8 + - - +
108C ILE* 4.3 9.0 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PHE* 3.4 11.6 - - - -
116B VAL* 2.9 36.7 + - + +
136B GLN* 3.1 5.7 - - + +
137B GLY* 1.3 80.6 - - - +
139B LEU* 1.3 66.0 + - - +
144B HIS* 3.3 43.1 - - + +
145B SER* 4.0 1.3 - - - +
107C ARG* 4.0 5.6 - - - +
108C ILE* 4.9 2.5 - - - -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ASP* 3.8 25.4 - - + -
114B VAL 3.5 9.6 - - - +
115B PHE* 3.8 37.5 - - + +
116B VAL* 4.2 2.7 - - - -
138B ALA* 1.3 77.2 - - - +
140B LEU* 1.3 70.6 + - - +
142B ASP* 3.4 19.2 + - + +
145B SER* 3.5 14.6 - - - -
169B PRO* 4.2 6.5 - - + -
107C ARG 5.2 1.4 + - - -
108C ILE* 3.4 40.8 - - + +
111C LYS* 4.3 12.1 - - + -
112C GLY* 3.6 18.2 - - - +
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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