Contacts of the strand formed by residues 142 - 152 (chain I) in PDB entry 1CL7
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 MET 142 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141I SER* 1.3 80.7 - - - +
143I VAL* 1.3 63.4 + - - +
144I THR* 4.1 1.8 + - - -
189I THR* 3.1 45.1 - - - +
190I VAL 3.4 9.6 - - - +
191I PRO* 4.0 12.6 - - + -
192I SER* 3.2 1.5 + - - -
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Residues in contact with VAL 143 (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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126H PRO* 4.1 12.6 - - + -
142I MET* 1.3 74.1 - - - +
144I THR* 1.3 58.7 + - - +
145I LEU* 3.5 25.5 + - + -
188I VAL 3.3 2.6 - - - +
189I THR* 2.9 2.5 - - - -
190I VAL* 2.5 48.2 + - + +
191I PRO 3.6 4.3 - - - +
192I SER* 3.1 38.8 - - - +
195I ARG* 4.1 14.4 - - + +
196I PRO* 5.0 3.4 - - + -
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Residues in contact with THR 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PRO* 3.8 6.3 - - - +
142I MET 4.1 2.1 + - - -
143I VAL* 1.3 71.5 - - - +
145I LEU* 1.3 75.4 - - - +
187I SER* 4.3 5.2 - - - -
188I VAL 3.3 5.4 - - - +
189I THR* 2.8 30.9 - - + +
114L THR* 5.0 5.9 - - - +
116L SER* 3.8 23.2 + - - +
118L PHE* 3.0 31.0 - - + -
135L PHE* 4.0 13.7 - - + -
137L ASN* 5.0 2.7 - - - +
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Residues in contact with LEU 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU 3.6 9.4 - - - +
126H PRO* 3.6 19.7 - - + -
143I VAL* 3.5 25.6 - - + -
144I THR* 1.3 86.1 - - - +
146I GLY* 1.3 59.7 + - - +
161I TRP* 4.2 4.7 - - + -
187I SER* 3.6 1.9 - - - -
188I VAL* 2.9 39.5 + - + +
190I VAL* 3.7 18.4 - - + -
195I ARG* 3.5 21.8 - - + +
200I VAL* 3.5 29.6 - - + -
217I ILE* 4.0 18.8 - - + -
118L PHE* 4.0 3.1 - - - -
135L PHE* 4.0 0.5 - - - -
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Residues in contact with GLY 146 (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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124H LEU* 3.1 40.0 + - - -
145I LEU* 1.3 76.8 - - - +
147I CYS* 1.3 61.8 + - - +
161I TRP* 3.2 14.9 - - - -
186I SER 3.1 13.0 - - - -
217I ILE* 4.0 7.3 - - - +
135L PHE* 3.8 4.7 - - - -
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Residues in contact with CYS 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 3.3 25.8 - - - -
122H TYR 3.5 7.4 - - - -
123H PRO* 5.2 1.3 - - - -
124H LEU* 3.2 7.6 - - - +
146I GLY* 1.3 74.7 - - - +
148I LEU* 1.3 62.0 + - - +
149I VAL* 3.5 4.3 + - - +
159I VAL* 4.7 0.9 - - + -
161I TRP* 3.7 10.3 - - + -
185I SER* 3.5 7.6 - - - -
186I SER* 3.0 27.7 + - - +
202I CYS* 2.0 49.4 - - - -
204I VAL* 4.1 3.1 - - - -
215I LYS* 5.7 0.4 - - - -
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Residues in contact with LEU 148 (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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120H SER 3.3 6.1 - - - +
121H VAL* 3.6 1.2 - - - -
122H TYR* 2.6 57.4 + - + +
124H LEU* 3.9 18.2 - - + +
147I CYS* 1.3 70.8 - - - +
149I VAL* 1.3 65.5 + - - +
150I LYS* 4.0 17.5 - - + -
183I THR* 4.0 11.2 - - + -
184I LEU 3.9 11.7 - - - +
185I SER* 4.0 8.5 - - - +
124L GLN* 3.8 12.3 - - - +
131L SER* 3.7 33.4 - - - +
133L VAL* 4.7 12.6 - - + -
178L THR* 5.6 4.3 - - + +
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Residues in contact with VAL 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 3.5 28.0 - - + -
120H SER 3.8 2.9 - - - -
121H VAL* 4.6 2.5 - - + +
147I CYS* 4.0 12.6 - - + +
148I LEU* 1.3 70.7 - - - +
150I LYS* 1.3 61.1 + - - +
152I TYR* 4.4 4.4 - - + -
157I VAL* 4.2 16.6 - - + -
159I VAL* 4.1 5.8 - - + -
183I THR* 3.6 1.9 - - - +
184I LEU* 2.6 60.7 + - + +
204I VAL* 3.6 40.2 - - + -
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Residues in contact with LYS 150 (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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119H PRO* 4.3 0.6 - - - +
120H SER* 2.8 48.0 + - - +
122H TYR* 4.8 7.6 - - + -
148I LEU* 4.0 18.6 - - + -
149I VAL* 1.3 78.7 - - - +
151I GLY* 1.3 66.2 + - - +
152I TYR 3.6 2.5 - - - -
178I GLN* 4.2 29.5 - - - +
182I TYR 4.3 2.0 - - - -
183I THR* 3.9 20.9 - - + +
124L GLN* 4.3 18.6 - - - +
131L SER* 4.3 14.6 - - - +
178L THR* 6.5 0.4 - - + -
180L THR* 5.1 7.0 - - - -
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Residues in contact with GLY 151 (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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117H THR* 3.3 15.2 - - - +
118H PRO 3.8 3.9 - - - +
120H SER* 4.9 1.3 - - - -
150I LYS* 1.3 84.6 - - - +
152I TYR* 1.3 58.8 + - - +
181I LEU* 3.2 35.1 - - - +
182I TYR 3.4 7.5 + - - -
183I THR* 4.1 1.8 + - - -
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Residues in contact with TYR 152 (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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117H THR 3.0 5.4 - - - +
119H PRO* 3.2 42.4 - - + -
149I VAL* 4.4 6.5 - - + -
150I LYS 3.6 0.2 - - - -
151I GLY* 1.3 80.8 - - - +
153I PHE* 1.3 61.5 + - - +
154I PRO 2.9 29.2 - - - -
155I GLU* 3.4 17.2 + - + +
156I PRO* 4.5 0.4 - - - +
157I VAL* 3.5 36.3 + - + +
175I ALA* 3.0 27.2 - - - +
181I LEU* 3.9 1.2 - - - -
182I TYR* 2.9 64.7 + - + +
183I THR* 4.2 2.2 - - - -
184I LEU* 3.9 13.8 - - + +
206I HIS* 3.5 9.4 - + - +
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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