Contacts of the strand formed by residues 173 - 182 (chain I) in PDB entry 3SKJ
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 TYR 173 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I THR* 5.5 5.9 - - - +
141I ASP* 3.1 22.5 + - - -
142I TYR* 2.9 47.7 + - + +
143I PHE* 3.6 30.4 - + - -
144I PRO* 4.5 0.9 - - + -
145I GLU* 3.5 54.3 - - + +
165I ALA* 3.9 7.0 - - + -
166I VAL 3.2 17.9 - - - +
167I LEU* 4.0 28.1 - - + +
168I GLN* 3.9 0.9 - - - -
172I LEU* 1.3 75.5 - - - +
174I SER* 1.3 60.5 + - - +
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Residues in contact with SER 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 3.5 20.8 - - - +
139I VAL 3.4 10.8 + - - -
140I LYS* 4.1 9.3 - - - +
142I TYR* 4.1 1.6 - - - -
164I PRO 4.5 0.7 - - - +
165I ALA* 3.3 2.1 - - - -
166I VAL* 2.9 40.5 + - - +
168I GLN* 3.8 26.9 + - - -
173I TYR* 1.3 75.7 - - - +
175I LEU* 1.3 63.5 + - - +
178M THR* 5.7 2.8 + - - +
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Residues in contact with LEU 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 3.5 2.8 - - - +
139I VAL* 2.6 59.7 + - + +
142I TYR* 3.8 24.9 - - + +
147I VAL* 4.2 19.5 - - + +
149I VAL* 4.0 15.3 - - + -
162I THR* 4.0 12.1 - - + -
163I PHE 3.4 23.3 - - - +
164I PRO 5.1 1.6 - - - -
165I ALA* 4.3 9.9 - - + +
174I SER* 1.3 76.5 + - - +
176I SER* 1.3 78.9 + - - +
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Residues in contact with SER 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 4.7 11.2 - - - -
137I CYS 3.3 9.4 - - - -
138I LEU* 4.0 13.2 - - - +
163I PHE* 3.0 41.9 + - - +
175I LEU* 1.3 83.3 + - - +
177I SER* 1.3 62.9 + - - +
178I VAL* 4.9 2.9 - - - -
133M VAL* 4.8 4.4 - - - +
176M SER* 3.6 23.6 + - - -
178M THR* 4.5 6.4 + - - -
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Residues in contact with SER 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I GLY* 3.0 2.8 - - - -
137I CYS* 2.7 41.4 + - - -
149I VAL* 3.7 26.8 - - - +
151I TRP* 3.1 24.4 + - - -
160I VAL* 4.0 0.9 - - - +
161I HIS 3.3 6.2 + - - -
162I THR* 3.0 24.8 + - - -
175I LEU* 4.2 0.8 - - - +
176I SER* 1.3 76.0 - - - +
178I VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 4.4 17.5 - - + -
135I LEU 3.2 12.8 - - - +
136I GLY* 4.0 0.2 - - - -
151I TRP* 4.7 0.4 - - - -
160I VAL* 3.2 4.9 - - - +
161I HIS* 2.7 67.1 + - + +
163I PHE* 3.9 15.9 - - + -
176I SER* 4.9 2.9 - - - -
177I SER* 1.3 80.9 + - - +
179I VAL* 1.3 68.1 + - - +
180I THR* 6.0 1.3 - - + -
118M PHE* 5.2 2.2 - - + -
133M VAL* 6.2 1.3 - - + -
135M LEU* 3.8 35.7 - - + -
137M ASN* 5.0 2.0 - - - +
176M SER* 6.0 0.7 - - - +
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Residues in contact with VAL 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I ALA 3.6 0.3 - - - +
134I ALA* 3.4 4.7 - - - +
135I LEU* 2.8 35.8 + - + +
151I TRP* 3.4 45.8 - - + +
156I LEU* 3.4 27.1 - - + -
158I SER 3.6 20.4 - - - +
159I GLY 3.4 10.3 - - - -
160I VAL* 3.8 4.5 - - + -
178I VAL* 1.3 79.1 - - - +
180I THR* 1.3 71.7 + - - +
181I VAL* 4.1 8.2 + - + -
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Residues in contact with THR 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I THR* 4.0 17.7 - - + -
133I ALA 3.1 8.7 - - - +
134I ALA* 4.9 7.9 - - + -
156I LEU* 5.9 0.3 - - - +
158I SER 4.2 6.6 - - - +
159I GLY* 3.4 18.1 + - - +
161I HIS* 5.5 0.6 - - - +
178I VAL* 6.0 2.5 - - + -
179I VAL* 1.3 84.6 - - - +
181I VAL* 1.3 65.0 + - - +
116M PHE* 5.0 5.8 - - + -
135M LEU* 6.1 1.1 - - + -
137M ASN* 3.5 35.5 + - + +
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Residues in contact with VAL 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I THR* 3.6 5.4 - - - -
133I ALA* 2.8 42.0 + - + +
135I LEU* 4.2 18.2 - - + -
156I LEU* 4.5 5.2 - - + -
179I VAL* 4.2 15.9 - - + -
180I THR* 1.3 81.6 - - - +
182I PRO* 1.3 80.3 - - + +
186I LEU* 4.0 23.6 - - + -
191I TYR* 3.9 31.2 - - + +
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Residues in contact with PRO 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I GLY 3.7 9.9 - - - +
132I THR* 4.7 2.0 - - - +
181I VAL* 1.3 91.8 - - + +
183I SER* 1.3 65.1 + - - +
184I SER* 3.2 12.7 + - - +
185I SER* 3.2 27.8 + - - +
186I LEU 4.2 1.2 + - - -
191I TYR* 5.2 1.8 - - - +
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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