Contacts of the strand formed by residues 135 - 143 (chain A) in PDB entry 3IAY
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A GLN* 3.9 10.7 + - + +
123A SER 3.4 11.7 - - - +
124A VAL* 3.6 18.3 - - + +
133A THR* 3.2 22.5 + - - +
134A SER* 1.3 81.3 + - - +
136A VAL* 1.3 68.2 + - - +
153A VAL 4.5 1.2 - - - +
155A GLY 4.6 4.5 + - - -
156A PHE 4.5 0.3 + - - +
219A THR 4.5 0.3 + - - -
220A TYR* 4.1 9.9 - - - +
221A PRO* 3.6 41.2 - - + +
254A TYR* 3.7 22.1 + - + +
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Residues in contact with VAL 136 (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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122A GLN* 3.5 5.0 - - - -
123A SER* 2.7 40.2 + - - +
125A LEU* 3.7 29.8 - - + -
133A THR 6.1 0.2 - - - +
134A SER 4.1 2.0 - - - +
135A THR* 1.3 81.1 - - - +
137A VAL* 1.3 64.9 - - - +
138A ARG* 3.8 28.3 - - + +
152A ASN* 4.1 9.2 - - + +
153A VAL 3.4 15.3 - - - +
154A THR* 3.8 26.9 - - + -
254A TYR* 3.8 8.5 - - - -
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Residues in contact with VAL 137 (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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120A ALA* 3.7 20.0 - - + -
121A GLU 3.6 6.3 - - - +
122A GLN* 5.0 0.2 - - - -
136A VAL* 1.3 73.8 - - - +
138A ARG* 1.3 62.3 + - - +
139A PHE* 3.3 31.0 + - + -
151A CYS 3.5 2.1 - - - +
153A VAL* 2.8 32.6 + - + +
254A TYR* 3.5 27.1 + - + -
255A THR* 4.0 17.9 - - + +
258A LEU* 3.5 32.5 - - + -
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Residues in contact with ARG 138 (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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120A ALA* 3.1 3.6 - - - -
121A GLU* 2.8 35.5 + - + +
123A SER* 3.2 27.3 + - - -
124A VAL 3.6 21.4 + - - -
125A LEU* 4.1 14.0 - - - +
126A ASN 5.4 0.6 - - - +
136A VAL* 3.8 12.6 - - + -
137A VAL* 1.3 72.1 - - - +
139A PHE* 1.3 60.7 + - - +
140A PHE* 3.8 12.3 - - + -
150A LEU* 3.6 24.0 - - + +
151A CYS 3.7 5.2 - - - -
152A ASN* 2.6 44.3 + - - +
286A VAL* 3.7 36.4 - - - +
292A GLU* 4.8 1.0 + - - -
429A LEU* 4.4 17.2 - - - +
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Residues in contact with PHE 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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115A PHE* 4.3 18.8 - - + -
117A GLN* 3.5 34.3 - - + -
119A ASP 3.4 1.6 - - - -
120A ALA* 3.5 17.9 - - + -
137A VAL* 3.3 28.5 - - + -
138A ARG* 1.3 73.2 - - - +
140A PHE* 1.3 62.5 + - - +
149A VAL 3.7 0.7 - - - +
150A LEU* 3.5 3.8 - - - +
151A CYS* 2.9 37.4 + - + +
153A VAL* 3.6 31.4 - - + -
258A LEU* 3.9 13.5 - - + -
259A MET* 4.1 12.8 - - + -
264A ILE* 3.8 31.0 - - + -
270A ILE* 4.2 5.2 - - + -
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Residues in contact with PHE 140 (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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115A PHE* 4.3 4.0 - - - -
117A GLN* 3.4 2.9 - - - -
118A ILE* 2.8 28.8 + - + +
119A ASP* 2.9 17.2 + - + +
120A ALA* 4.9 0.2 - - - -
121A GLU* 4.3 13.7 - - + -
138A ARG* 3.8 23.1 - - + -
139A PHE* 1.3 76.2 - - - +
141A GLY* 1.3 57.7 + - - +
149A VAL 3.2 5.8 - - - +
150A LEU* 3.8 26.5 - - + -
289A CYS* 4.1 19.5 - - - -
428A ARG* 4.0 22.4 - - + +
429A LEU* 4.0 31.4 - - + -
458A GLY* 3.4 44.9 - - - +
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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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115A PHE* 3.8 10.1 - - - -
116A GLN 3.1 13.5 - - - -
118A ILE* 4.3 8.7 - - - -
140A PHE* 1.3 75.6 - - - +
142A VAL* 1.3 68.6 + - - +
148A SER* 3.3 6.8 - - - -
149A VAL* 2.9 31.9 + - - -
396A ASP* 4.6 1.3 - - - +
428A ARG* 4.7 3.9 + - - +
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Residues in contact with VAL 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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99A ARG* 4.0 10.8 - - - +
115A PHE* 3.3 6.7 - - - +
116A GLN 2.8 31.1 + - - -
118A ILE* 5.4 0.4 - - + -
141A GLY* 1.3 78.8 - - - +
143A THR* 1.3 75.0 + - - +
146A GLY* 3.7 20.9 - - - -
147A HIS 3.3 7.4 - - - +
148A SER* 5.0 0.2 - - - -
269A TRP* 4.2 0.2 - - - -
313A ALA* 3.4 20.3 - - + +
314A PRO* 4.3 11.0 - - + +
315A LEU* 3.7 10.1 - - + -
396A ASP* 2.9 40.4 - - - +
428A ARG* 4.6 0.4 - - - +
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Residues in contact with THR 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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113A ILE* 4.1 11.2 - - + -
114A SER 3.4 22.7 - - - +
115A PHE* 4.0 1.8 - - + +
142A VAL* 1.3 77.6 - - - +
144A SER* 1.3 65.8 + - - +
145A GLU* 2.6 25.4 + - - +
146A GLY 3.0 10.2 + - - -
147A HIS* 2.9 40.8 + - + +
149A VAL* 3.7 19.7 - - + -
269A TRP* 4.3 1.6 - - - -
291A LEU* 4.7 3.8 - - + -
314A PRO* 3.3 11.1 - - - +
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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