Contacts of the strand formed by residues 104 - 114 (chain A) in PDB entry 1CKQ
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 TRP 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A SER* 3.7 31.9 - - - -
55A PHE 4.6 1.3 - - - -
56A ARG* 3.5 77.2 - - + +
96A GLU* 3.8 18.8 - - + +
97A VAL 3.4 19.5 - - - -
98A LYS* 3.8 30.1 - - + +
102A GLY 4.5 6.3 + - - -
103A GLU* 1.3 96.2 + - - +
105A ARG* 1.3 64.5 + - - +
106A VAL 4.3 0.7 + - - -
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Residues in contact with ARG 105 (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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96A GLU* 3.4 2.9 - - - -
97A VAL* 2.8 36.2 + - + +
99A ASP* 3.0 35.2 + - + +
101A TYR* 5.3 0.6 - - - -
103A GLU* 3.9 9.0 - - - +
104A TRP* 1.3 80.3 - - - +
106A VAL* 1.3 64.5 + - - +
107A VAL* 3.4 4.2 + - - +
159A SER 5.9 0.2 + - - -
160A GLU* 2.9 43.9 + - - +
162A HIS* 5.5 0.2 - - + -
266A LEU* 3.5 39.6 - - + +
269A ASP* 3.0 33.1 + - - +
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Residues in contact with VAL 106 (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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94A ILE* 4.2 5.8 - - + -
95A VAL 3.6 8.1 - - - +
96A GLU* 3.8 12.6 + - + +
104A TRP 4.2 0.8 - - - -
105A ARG* 1.3 70.6 - - - +
107A VAL* 1.3 62.3 + - - +
108A LEU 3.7 12.3 - - - +
109A VAL* 3.8 26.0 - - + -
153A ILE* 5.9 0.4 - - + -
156A PHE* 4.4 18.6 - - + -
157A MET* 3.4 43.4 - - + +
160A GLU* 5.5 3.3 + - + +
162A HIS* 3.0 25.8 + - - -
164A PRO* 4.0 3.6 - - + -
266A LEU* 4.7 0.3 - - - +
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Residues in contact with VAL 107 (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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46A LEU* 4.6 6.7 - - + -
55A PHE* 4.8 2.7 - - + -
95A VAL* 2.8 14.6 + - + +
96A GLU 4.1 2.7 - - - -
97A VAL* 3.6 40.8 - - + +
105A ARG 3.6 5.2 - - - +
106A VAL* 1.3 74.3 - - - +
108A LEU* 1.3 63.0 + - - +
164A PRO* 3.2 8.3 - - - +
259A SER* 3.2 43.5 - - - +
262A SER* 2.8 28.2 + - - -
263A LEU* 4.2 13.0 - - + -
266A LEU* 4.7 4.0 - - + -
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Residues in contact with LEU 108 (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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39A SER* 4.6 2.5 - - - +
42A VAL* 4.2 8.3 - - + -
93A GLY 4.1 0.2 - - - +
94A ILE* 3.3 6.2 - - - +
95A VAL* 2.9 52.3 + - + -
106A VAL* 3.7 1.8 - - - +
107A VAL* 1.3 81.6 - - - +
109A VAL* 1.3 77.4 + - - +
110A ALA* 4.6 1.8 - - + +
164A PRO* 3.8 7.6 - - - +
166A VAL* 3.6 30.5 - - + -
255A MET* 3.9 45.5 - - + +
258A ILE* 4.3 6.5 - - + -
259A SER* 3.4 18.8 - - - +
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Residues in contact with VAL 109 (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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90A PRO* 4.1 20.6 - - + -
93A GLY 3.6 11.9 - - - +
94A ILE* 4.0 14.1 - - + -
106A VAL* 3.8 20.4 - - + -
108A LEU* 1.3 81.2 - - - +
110A ALA* 1.3 61.5 + - - +
153A ILE* 4.2 23.6 - - + -
164A PRO* 3.1 11.9 + - + +
165A TYR* 3.5 32.3 - - + -
166A VAL* 2.9 27.4 + - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.6 22.9 - - + -
39A SER* 3.9 6.9 + - - +
90A PRO* 3.7 11.3 - - - +
92A GLY* 3.0 22.9 + - - -
93A GLY 3.5 6.5 + - - -
108A LEU* 4.3 3.9 - - + +
109A VAL* 1.3 75.5 - - - +
111A GLU* 1.3 64.3 + - - +
165A TYR* 5.4 0.2 - - - -
166A VAL* 3.4 11.7 - - + +
168A PHE* 5.1 1.3 - - + -
255A MET* 3.8 23.6 - - + -
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Residues in contact with GLU 111 (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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35A VAL* 4.4 3.6 - - - +
89A LYS 4.6 1.4 - - - +
90A PRO* 3.8 12.3 - - - +
91A ASP* 2.9 32.6 + - - +
92A GLY 4.5 0.2 - - - +
110A ALA* 1.3 75.2 - - - +
112A ALA* 1.3 63.3 + - - +
113A LYS* 3.7 35.0 + - - -
146A SER* 6.2 0.2 - - - -
149A ASN* 3.2 20.6 + - - +
165A TYR* 2.8 31.2 + - + +
166A VAL 2.9 8.7 + - - +
167A LEU* 3.4 16.3 - - + -
168A PHE* 2.9 28.8 + - - -
5B G 5.5 1.6 - - - +
6B A 4.2 3.3 + - - -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.0 19.3 - - + -
91A ASP* 3.1 26.3 + - - +
111A GLU* 1.3 75.1 - - - +
113A LYS* 1.3 68.8 + - - +
114A HIS* 4.6 20.1 + - + +
168A PHE* 3.4 17.5 - - + +
251A MET* 5.8 2.9 - - - -
6B A 4.5 2.9 + - - -
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Residues in contact with LYS 113 (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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111A GLU* 3.7 27.0 + - + -
112A ALA* 1.3 79.5 - - - +
114A HIS* 1.3 73.5 + - - +
143A ILE* 3.5 22.9 - - + -
145A ARG* 4.0 13.7 - - - +
146A SER* 3.6 32.3 - - - +
149A ASN* 5.4 3.2 - - - +
167A LEU* 3.7 17.0 - - + -
168A PHE 2.9 10.0 + - - +
169A LEU* 3.7 6.4 - - + -
170A GLU* 3.2 19.6 + - - +
174A PHE* 5.2 0.4 - - - -
5B G 5.2 0.8 - - - -
6B A 2.9 33.2 + - - +
7B A 5.6 0.4 - - - -
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Residues in contact with HIS 114 (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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112A ALA* 4.6 20.4 + - + +
113A LYS* 1.3 92.6 + - - +
115A GLN* 1.3 65.8 + - - +
143A ILE* 5.5 0.9 - - - +
168A PHE 5.7 0.2 - - - -
170A GLU* 3.3 40.2 - - + +
174A PHE* 4.5 1.1 - - - -
246A TRP* 6.2 0.2 - + - -
7B A 3.5 49.6 + - - +
8B T 5.1 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