Contacts of the strand formed by residues 113 - 121 (chain C) in PDB entry 2R7D
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 LEU 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C ASP* 3.4 6.6 - - - +
109C LEU* 2.7 49.8 + - + +
110C GLY 3.0 13.2 + - - +
111C GLY 3.1 5.8 + - - +
112C GLY* 1.3 77.9 - - - +
114C THR* 1.3 55.0 + - - +
178C ASP* 4.1 14.1 - - + -
179C LEU 3.3 25.4 - - - +
180C ASP* 3.6 7.0 - - + +
186C GLU* 3.1 45.3 - - + +
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 4.2 4.7 - - + -
107C GLU 3.6 11.4 - - - +
108C ASP* 4.7 6.2 + - - +
109C LEU* 4.5 1.3 - - - -
112C GLY 3.6 5.6 + - - -
113C LEU* 1.3 78.0 + - - +
115C ARG* 1.3 65.0 + - - +
116C LEU 3.8 0.3 + - - -
177C LEU 3.4 1.7 - - - +
178C ASP* 4.4 1.8 - - - -
179C LEU* 2.7 46.4 + - - +
218C THR* 3.7 26.2 - - + -
221C ARG* 3.1 21.7 + - - -
222C LEU* 3.8 24.2 - - + -
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Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 3.2 8.1 - - - +
107C GLU* 2.8 53.9 + - + +
109C LEU* 3.9 29.7 - - + +
114C THR* 1.3 73.7 - - - +
116C LEU* 1.3 65.8 + - - +
117C TRP* 3.5 41.5 + - + +
176C CYS* 4.2 13.2 - - + -
177C LEU 3.2 5.4 - - - +
178C ASP* 2.7 41.0 + - - +
189C ASP* 4.7 7.9 + - - -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 5.0 0.4 - - + -
105C GLY 3.6 10.5 - - - +
106C VAL* 4.1 4.7 - - + -
114C THR 3.8 1.2 + - - -
115C ARG* 1.3 73.0 - - - +
117C TRP* 1.3 73.2 + - - +
118C VAL* 4.1 16.6 - - + -
175C ILE 3.7 0.9 - - - +
176C CYS* 3.1 6.9 - - - +
177C LEU* 2.7 43.5 + - + +
179C LEU* 4.4 9.9 - - + -
219C LEU* 3.8 24.0 - - + -
222C LEU* 4.2 15.7 - - + -
269C CYS* 4.1 13.9 - - - -
272C LEU* 3.4 43.1 - - + -
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Residues in contact with TRP 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 4.0 18.2 - - + -
84C LEU* 3.6 30.1 - - + -
87C LEU* 4.1 9.8 - - + +
104C VAL* 3.4 5.5 - - - -
105C GLY* 2.8 39.6 + - - +
106C VAL 4.6 2.2 - - - -
107C GLU* 2.7 37.2 + - + -
115C ARG* 3.5 32.3 - - + +
116C LEU* 1.3 76.3 - - - +
118C VAL* 1.3 63.6 + - - +
119C HIS* 3.5 31.0 - + - +
174C SER* 3.9 21.5 - - - -
175C ILE 3.7 2.2 - - - -
176C CYS* 3.5 27.1 - - + -
191C LEU* 4.0 17.7 - - + -
193C THR* 4.3 1.3 - - + -
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASP* 5.1 0.2 - - + -
103C ALA 3.5 4.9 - - - +
104C VAL* 4.3 1.8 - - + -
116C LEU* 4.1 18.8 - - + -
117C TRP* 1.3 78.3 - - - +
119C HIS* 1.3 62.9 + - - +
120C VAL* 4.5 4.3 - - + -
174C SER* 3.5 1.2 - - - -
175C ILE* 2.9 39.5 + - - +
177C LEU* 5.2 2.0 - - + -
269C CYS* 3.6 26.5 - - + +
270C MSE 3.8 22.2 - - + -
273C ALA* 3.5 29.6 - - + -
339C THR* 4.0 11.2 - - + -
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Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 3.6 21.7 - - + +
87C LEU* 6.1 2.0 - - + +
89C THR* 3.4 35.9 + - + +
102C ASP* 3.2 6.9 - - - +
103C ALA* 2.9 39.3 + - + +
104C VAL* 4.6 0.9 - - - -
105C GLY* 4.9 2.0 + - - -
117C TRP* 3.5 35.3 - + + +
118C VAL* 1.3 69.6 - - - +
120C VAL* 1.3 65.3 + - - +
164C LEU* 3.4 9.4 - - + +
172C ALA* 4.1 10.5 - - + -
173C LEU 4.1 0.2 - - - -
174C SER* 2.7 27.6 + - - +
195C VAL* 3.6 26.5 - - + +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASP 3.2 11.9 - - - +
102C ASP* 5.0 0.4 - - + -
118C VAL* 4.2 2.7 - - + +
119C HIS* 1.3 81.8 - - - +
121C ALA* 1.3 70.6 + - - +
122C ASP 3.1 0.9 + - - -
164C LEU* 3.9 4.7 - - - -
172C ALA* 3.2 4.4 - - - +
173C LEU 3.0 36.3 + - - +
175C ILE* 4.1 15.5 - - + -
338C ALA 3.7 13.0 - - - +
339C THR* 3.9 23.3 - - + +
341C PRO* 3.4 30.3 - - + -
351C HIS* 3.4 17.5 - - + +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C PRO 4.6 1.8 - - - +
101C ASP* 2.8 24.6 + - - +
120C VAL* 1.3 72.5 - - - +
122C ASP* 1.3 57.7 + - - +
123C VAL* 2.9 12.9 + - + -
162C ALA* 3.6 24.2 - - + +
164C LEU* 3.8 8.5 - - - +
341C PRO* 3.6 4.1 - - + +
342C MSE 4.0 29.6 - - + -
351C HIS* 3.3 16.6 - - - -
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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