Contacts of the strand formed by residues 170 - 178 (chain A) in PDB entry 3SE3
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LYS* 3.6 2.3 - - - +
145A ASN* 2.7 66.7 + - + +
168A GLU 4.3 0.6 + - - -
169A THR* 1.3 70.7 - - - +
171A TYR* 1.3 64.3 + - - +
193A CYS* 4.0 12.1 - - + -
194A ILE 3.1 10.8 - - - +
195A LYS* 3.2 19.2 + - - +
410A NAG 5.1 10.9 - - + +
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 4.3 12.1 - - + -
142A ILE* 3.9 24.2 - - + -
143A TRP 3.4 15.7 - - - +
144A LYS* 4.2 16.2 - - + -
165A LEU* 3.3 23.9 - - + +
166A SER* 2.9 34.3 + - - -
169A THR* 3.0 35.8 - - - -
170A THR* 1.3 73.9 - - - +
172A CYS* 1.3 63.4 + - - +
173A LEU* 5.6 1.3 - - + +
192A HIS 3.9 0.7 - - - +
193A CYS* 3.1 22.9 - - - +
194A ILE* 2.9 14.9 + - - +
196A THR* 3.6 22.2 - - + -
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Residues in contact with CYS 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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142A ILE* 3.0 16.8 - - - +
143A TRP* 2.9 43.6 + - + +
145A ASN* 3.1 27.8 - - - -
171A TYR* 1.3 74.8 - - - +
173A LEU* 1.3 69.3 + - - +
191A VAL* 3.9 3.1 - - + -
192A HIS 3.4 5.2 - - - -
193A CYS* 2.0 43.7 - - - -
410A NAG 5.3 0.9 - - - -
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Residues in contact with LEU 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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106A VAL* 4.5 16.2 - - + -
108A LEU* 4.3 20.2 - - + -
115A ILE* 5.7 7.0 - - + -
117A ILE* 5.7 5.4 - - + -
140A LEU* 5.1 6.7 - - + -
141A VAL 3.4 15.5 - - - +
142A ILE* 3.9 24.7 - - + -
143A TRP* 3.8 4.3 - - - -
162A ILE* 5.9 2.5 - - + -
171A TYR 5.6 1.8 - - - +
172A CYS* 1.3 80.3 - - - +
174A LYS* 1.3 68.1 + - - +
175A VAL* 4.1 17.9 - - + -
190A PRO 3.8 0.2 - - - +
191A VAL* 3.0 8.2 - - - +
192A HIS* 2.7 49.7 + - + +
194A ILE* 6.5 0.2 - - + -
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Residues in contact with LYS 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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140A LEU* 3.2 18.7 - - - +
141A VAL* 3.4 16.9 + - + +
143A TRP* 4.9 7.0 - - + -
173A LEU* 1.3 76.7 - - - +
175A VAL* 1.3 64.2 + - - +
188A TYR* 3.0 53.2 - - + +
189A SER* 3.6 21.1 - - - +
190A PRO 4.0 1.1 - - - +
191A VAL* 3.8 21.5 - - + -
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Residues in contact with VAL 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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104A PRO* 3.6 14.8 - - + +
106A VAL* 3.6 27.1 - - + -
117A ILE* 5.7 2.0 - - + -
119A ILE* 4.1 23.1 - - + -
138A TYR* 4.1 6.3 - - + -
139A SER 3.9 9.0 - - - +
140A LEU* 4.0 18.4 - - + -
173A LEU* 4.1 12.6 - - + -
174A LYS* 1.3 78.5 - - - +
176A LYS* 1.3 71.4 + - - +
188A TYR* 3.2 6.0 - - - -
189A SER* 2.6 42.4 + - - +
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Residues in contact with LYS 176 (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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104A PRO* 4.0 1.8 - - - -
138A TYR* 3.7 1.0 - - - -
139A SER* 3.0 51.2 + - - +
152A ARG* 5.3 8.9 - - - +
154A GLU* 6.6 0.2 - - - -
175A VAL* 1.3 80.3 - - - +
177A ALA* 1.3 63.5 + - - +
185A ILE* 4.1 19.2 - - + +
186A GLY 3.6 22.0 + - - +
187A VAL 3.7 7.0 - - - +
188A TYR* 3.1 53.4 + - + -
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Residues in contact with ALA 177 (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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101A ILE* 3.6 27.6 - - + -
102A GLY 4.5 0.2 - - - +
104A PRO* 3.8 13.9 - - + +
121A PRO* 6.4 0.4 - - + -
136A PHE* 4.5 8.7 - - + -
137A THR 4.0 3.1 - - - +
138A TYR* 3.9 24.5 - - + -
176A LYS* 1.3 77.6 - - - +
178A ALA* 1.3 61.5 + - - +
185A ILE* 3.6 3.1 - - - +
186A GLY* 2.8 28.9 + - - -
187A VAL 4.1 3.0 + - - -
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Residues in contact with ALA 178 (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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101A ILE* 3.8 9.9 - - - -
136A PHE* 3.5 7.6 - - - -
137A THR* 2.6 47.3 + - + +
138A TYR 5.4 0.2 - - - -
139A SER* 4.6 11.4 - - - +
177A ALA* 1.3 77.5 - - - +
179A LEU* 1.3 61.8 + - - +
180A LEU* 4.1 0.9 - - - +
185A ILE* 3.6 24.7 - - + -
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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