Contacts of the strand formed by residues 113 - 122 (chain E) in PDB entry 2Q6W
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 ASN 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLU* 5.5 2.2 - - - -
103E PRO* 3.7 10.1 - - - +
104E ALA* 3.6 2.0 - - - +
105E LYS* 3.1 45.5 + - - +
107E GLN* 3.9 20.2 - - + +
108E PRO 5.4 0.4 - - - +
111E HIS 3.5 1.5 + - - +
112E HIS* 1.3 78.2 + - - +
114E LEU* 1.3 89.2 + - - +
115E LEU* 6.3 0.7 - - + -
161E LEU 3.6 0.2 - - - +
162E GLU* 3.6 3.6 - - - -
163E THR* 2.7 43.2 + - - +
165E PRO* 4.2 15.5 - - + +
188E TRP* 5.8 1.6 - - - -
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Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A HIS* 3.4 25.8 - - + +
179A GLU* 3.4 26.5 - - - +
103E PRO* 3.2 4.3 - - - +
104E ALA* 2.4 53.8 + - + -
105E LYS* 6.2 1.1 - - + -
113E ASN* 1.3 80.3 + - - +
115E LEU* 1.3 59.1 + - - +
143E VAL* 4.7 2.7 - - + -
160E MET* 4.0 29.2 - - + -
161E LEU 3.3 4.7 - - - +
162E GLU* 3.4 38.6 - - + +
163E THR* 4.5 0.2 - - - -
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E VAL* 4.0 2.5 - - + -
102E TYR 4.0 2.5 - - - -
103E PRO* 3.9 18.6 - - + -
113E ASN* 3.9 1.9 - - + -
114E LEU* 1.3 74.1 - - - +
116E VAL* 1.3 62.2 + - - +
131E TRP* 3.6 21.2 - - + -
160E MET* 3.0 2.9 - - - -
161E LEU* 2.7 42.2 + - + +
163E THR* 3.6 15.9 - - + +
171E TYR* 3.3 47.3 - - + -
188E TRP* 3.5 40.6 - - + -
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E THR 3.4 1.0 - - - +
101E VAL* 2.9 9.5 - - - +
102E TYR* 2.6 79.8 + - + +
104E ALA* 4.1 17.9 - - + -
115E LEU* 1.3 75.0 - - - +
117E CYS* 1.3 62.0 + - - +
118E SER 3.6 9.2 - - - +
131E TRP* 3.8 2.2 - - - -
158E LEU* 4.1 16.6 - - + -
159E VAL 3.9 2.0 - - - -
160E MET* 3.7 29.2 - - + +
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Residues in contact with CYS 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL* 3.5 23.6 - - - -
100E THR 3.6 1.6 - - - -
101E VAL* 4.0 2.2 - - - -
116E VAL* 1.3 72.9 - - - +
118E SER* 1.3 63.3 + - - +
119E VAL* 3.6 12.6 + - - +
129E VAL* 4.3 2.7 - - + -
131E TRP* 3.5 11.4 - - + +
157E THR 3.7 0.3 - - - +
158E LEU* 3.2 2.3 - - - -
159E VAL* 2.7 45.7 + - - +
173E CYS* 2.0 50.5 - - - -
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Residues in contact with SER 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D SER* 5.2 0.3 - - - -
96D PRO* 3.0 40.3 - - - +
98E GLN 3.3 2.1 - - - +
99E VAL* 3.3 4.3 - - - +
100E THR* 2.8 40.4 + - - -
102E TYR* 3.8 15.0 + - - -
116E VAL* 3.6 1.2 - - - +
117E CYS* 1.3 73.2 - - - +
119E VAL* 1.3 61.3 + - - +
120E SER* 4.0 4.4 + - - -
156E GLN* 5.3 1.6 + - - -
157E THR 3.7 4.4 + - - -
158E LEU* 4.2 14.5 - - - +
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Residues in contact with VAL 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E PRO* 3.5 20.4 - - + -
98E GLN 3.3 2.5 - - - -
99E VAL* 4.2 3.6 - - + -
117E CYS* 3.7 27.1 - - - +
118E SER* 1.3 79.1 + - - +
120E SER* 1.3 60.0 + - - +
122E PHE* 3.3 4.0 - - + -
127E ILE* 3.4 32.8 - - + -
129E VAL* 3.9 12.6 - - + -
156E GLN* 3.1 2.8 - - - +
157E THR* 2.8 46.5 + - + +
175E VAL* 3.7 18.2 - - + -
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Residues in contact with SER 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN 3.5 22.2 - - - -
95D SER* 4.0 17.7 - - - -
96D PRO* 4.0 7.1 - - - +
97E PRO* 3.4 1.6 - - - +
98E GLN* 2.7 52.9 + - - +
118E SER* 4.4 5.2 + - - -
119E VAL* 1.3 76.0 - - - +
121E GLY* 1.3 65.4 + - - +
122E PHE* 3.3 4.4 + - - -
155E PHE 3.6 4.9 - - - -
156E GLN* 3.8 7.4 - - - -
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Residues in contact with GLY 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN 4.8 2.1 + - - -
95E VAL* 3.0 26.3 - - - +
96E HIS 3.5 4.9 - - - +
98E GLN* 5.3 1.6 - - - -
120E SER* 1.3 77.5 - - - +
122E PHE* 1.3 59.3 + - - +
150E ASN* 4.9 1.4 + - - -
154E THR* 3.6 20.3 - - - +
155E PHE 2.9 8.8 + - - -
156E GLN* 4.6 0.6 - - - +
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Residues in contact with PHE 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E VAL 3.4 12.8 - - - +
97E PRO* 3.8 14.6 - - + -
119E VAL* 3.3 28.0 - - + -
120E SER 3.8 9.9 - - - -
121E GLY* 1.3 79.1 - - - +
123E TYR* 1.3 62.4 + - - +
124E PRO 3.2 18.2 - - - -
125E GLY 2.8 25.4 - - - -
127E ILE* 3.7 29.2 - - + -
147E LEU* 3.7 13.7 - - + -
154E THR* 3.1 4.7 - - - -
155E PHE* 2.7 62.1 + - + -
156E GLN* 3.6 6.3 - - - -
157E THR* 4.0 2.0 - - + -
177E HIS* 3.5 13.5 - + + +
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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