Contacts of the strand formed by residues 129 - 139 (chain B) in PDB entry 4ZFO
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 THR 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LYS* 4.4 10.5 - - - +
124B GLN* 3.3 46.9 + - - +
125B LEU* 3.7 6.9 + - - +
127B SER* 3.5 6.4 + - - -
128B GLY* 1.3 80.5 + - - +
130B ALA* 1.3 63.8 + - - +
180B THR* 3.8 22.2 - - + -
181B LEU 3.5 13.0 + - - +
182B SER* 5.2 1.1 - - - -
183B LYS* 4.0 2.6 - - - +
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Residues in contact with ALA 130 (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* 3.9 17.0 - - + -
125B LEU* 3.9 4.9 - - + -
129B THR* 1.3 73.9 - - - +
131B SER* 1.3 61.9 + - - +
132B VAL* 4.0 1.1 - - + -
179B LEU 3.5 1.7 - - - +
180B THR* 3.4 4.7 - - - +
181B LEU* 2.8 43.7 + - + +
182B SER 4.5 1.1 - - - +
183B LYS 4.3 0.4 - - - +
186B TYR* 3.6 42.0 - - + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 5.7 1.4 - - - +
148A LEU* 3.5 19.6 - - - +
150A LYS* 3.6 16.6 + - - +
118B PHE 4.3 0.3 - - - +
119B PRO 4.1 1.4 - - - +
120B PRO* 3.3 22.0 - - - +
124B GLN* 2.7 36.1 + - - +
129B THR* 4.5 0.9 - - - +
130B ALA* 1.3 73.9 + - - +
132B VAL* 1.3 61.6 + - - +
133B VAL* 4.1 4.7 + - - +
178B THR* 4.0 15.2 - - - +
179B LEU 3.4 4.5 - - - -
180B THR* 4.2 5.9 + - - -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 4.3 2.7 - - + -
118B PHE 3.5 9.6 - - - +
119B PRO* 4.4 0.2 - - + -
120B PRO* 4.1 13.5 - - + -
130B ALA 4.8 0.9 - - - +
131B SER* 1.3 76.3 - - - +
133B VAL* 1.3 61.4 + - - +
148B TRP* 3.5 28.3 - - + -
178B THR* 3.3 3.1 - - - -
179B LEU* 2.8 46.6 + - + +
181B LEU* 4.4 15.9 - - + -
186B TYR* 4.3 15.0 - - + -
192B TYR* 4.5 5.8 - - + -
209B PHE* 3.5 32.5 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.8 30.5 - - + -
148A LEU* 4.6 9.2 - - + -
186A SER* 4.3 18.8 - - - +
188A VAL* 5.9 2.0 - - + -
117B ILE* 3.4 3.1 - - - +
118B PHE* 2.7 50.5 + - + -
131B SER 4.6 5.2 - - - +
132B VAL* 1.3 78.3 - - - +
134B CYS* 1.3 73.9 + - - +
135B LEU* 4.7 2.0 - - + +
148B TRP* 4.0 1.8 - - - -
176B SER* 4.7 9.9 - - - -
177B SER 3.5 5.6 - - - +
178B THR* 3.9 22.4 - - + +
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Residues in contact with CYS 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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115B VAL* 3.8 13.5 - - - -
116B PHE 3.4 5.6 - - - -
117B ILE* 4.4 1.8 - - + +
133B VAL* 1.3 76.5 - - - +
135B LEU* 1.3 63.9 + - - +
136B LEU* 3.8 16.7 - - - +
146B VAL* 4.8 0.2 - - - -
148B TRP* 3.6 14.3 - - + -
175B LEU 3.8 0.5 - - - +
176B SER* 3.3 5.9 - - - -
177B SER* 2.9 36.6 + - - +
194B CYS* 2.0 52.5 - - + -
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Residues in contact with LEU 135 (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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144A ALA* 4.1 15.0 - - + -
173A PHE* 3.6 28.5 - - + -
188A VAL* 3.8 28.3 - - + -
190A THR* 5.5 0.9 - - + -
114B SER 3.4 1.0 - - - +
115B VAL* 3.2 8.3 - - - +
116B PHE* 2.8 58.7 + - + +
118B PHE* 4.3 11.7 - - + -
133B VAL* 4.2 3.3 - - + -
134B CYS* 1.3 73.6 - - - +
136B LEU* 1.3 80.0 + - - +
137B ASN* 4.0 17.7 - - + +
175B LEU 3.5 9.9 - - - +
176B SER* 4.6 1.8 - - - +
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Residues in contact with LEU 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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113B PRO* 3.8 11.0 - - + -
114B SER 3.6 3.8 - - - -
115B VAL* 4.5 1.8 - - + -
134B CYS* 3.8 13.5 - - - +
135B LEU* 1.3 79.2 - - - +
137B ASN* 1.3 60.3 + - - +
139B PHE* 3.4 14.8 - - + -
144B ALA* 4.1 21.1 - - + -
146B VAL* 3.5 31.2 - - + -
174B SER* 3.2 6.6 - - - -
175B LEU* 2.8 53.3 + - + +
177B SER 5.8 0.2 - - - +
196B VAL* 3.6 42.8 - - + -
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Residues in contact with ASN 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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169A GLY 5.4 0.4 + - - -
171A HIS* 3.1 17.2 - - - -
188A VAL* 4.6 1.9 - - - +
190A THR* 3.5 27.0 + - - +
112B ALA 4.3 0.2 - - - +
113B PRO* 3.6 1.1 - - - +
114B SER* 2.9 41.0 + - - +
116B PHE* 4.4 7.2 - - + -
135B LEU* 4.0 24.0 - - + +
136B LEU* 1.3 73.7 - - - +
138B ASN* 1.3 95.1 + - - +
139B PHE* 3.5 1.9 + - - -
174B SER* 2.8 22.1 + - - -
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Residues in contact with ASN 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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169A GLY* 6.3 1.2 - - - -
171A HIS* 2.8 30.6 + - - -
190A THR* 5.1 4.6 + - - -
111B ALA* 3.9 7.3 - - - +
112B ALA 3.8 8.1 - - - +
114B SER* 6.0 0.2 - - - +
137B ASN* 1.3 89.8 + - - +
139B PHE* 1.3 59.0 + - - +
170B ASP* 4.2 11.9 + - - +
172B THR* 3.4 29.7 + - + +
173B TYR 3.1 7.2 + - - -
174B SER* 2.9 8.7 + - - -
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Residues in contact with PHE 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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111B ALA* 3.1 16.2 - - - +
113B PRO* 3.5 32.3 - - + -
136B LEU* 3.4 32.8 - - + -
138B ASN* 1.3 75.5 - - - +
140B TYR* 1.3 64.4 + - - +
141B PRO 3.2 19.7 - - - -
142B ARG* 3.2 31.0 - - - -
144B ALA* 3.9 12.6 - - + -
163B VAL* 4.9 2.7 - - + -
172B THR* 3.4 2.4 - - - -
173B TYR* 2.8 61.4 + - + +
174B SER 4.1 1.1 - - - -
175B LEU* 3.6 25.1 - - + -
198B HIS* 3.6 9.2 - + - +
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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