Contacts of the strand formed by residues 114 - 125 (chain A) in PDB entry 4KXA
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 THR 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LEU* 2.7 53.4 + - - +
112A GLU* 3.7 16.3 - - + +
113A ASP* 1.3 84.0 - - - +
115A TYR* 1.3 61.1 + - - +
194A GLY 3.5 8.5 - - - +
195A TRP* 3.8 21.5 - - + +
196A LEU* 3.4 10.3 - - - +
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Residues in contact with TYR 115 (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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106A VAL* 4.6 8.1 - - + -
107A LYS 3.3 14.4 - - - +
108A PRO* 3.7 9.9 - - + -
109A LEU* 4.3 1.1 - - - +
114A THR* 1.3 78.9 - - - +
116A THR* 1.3 74.6 + - - +
139A THR* 3.1 6.3 + - - -
192A PHE* 4.0 15.3 - + - -
193A ALA* 3.4 4.5 - - - +
194A GLY* 3.0 56.7 + - - +
195A TRP 3.6 12.1 - - - -
196A LEU* 3.7 17.0 - - + -
203A PHE* 3.6 36.9 + + + +
229A LYS* 3.0 16.1 + - - +
230A SER* 2.6 34.2 + - - -
289A PHE* 6.2 0.2 - + - -
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Residues in contact with THR 116 (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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105A HIS* 5.9 0.2 - - - -
106A VAL* 3.3 5.0 - - - +
107A LYS* 2.7 49.2 + - - +
109A LEU* 5.9 1.6 - - - +
114A THR* 6.5 0.2 - - - -
115A TYR* 1.3 84.7 - - - +
117A GLY* 1.3 58.1 + - - +
142A THR* 6.0 1.1 - - + +
192A PHE 3.4 11.2 - - - +
193A ALA* 4.2 12.1 - - + -
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Residues in contact with GLY 117 (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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105A HIS* 2.9 18.6 - - - -
106A VAL* 4.1 0.2 - - - -
107A LYS 4.8 0.2 - - - -
116A THR* 1.3 77.7 - - - +
118A THR* 1.3 64.1 + - - +
191A GLU* 3.5 3.1 - - - +
192A PHE* 2.9 50.5 + - - +
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Residues in contact with THR 118 (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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103A ASP 3.8 1.6 - - - +
104A LEU* 4.2 0.2 - - - +
105A HIS* 3.0 43.1 + - + +
117A GLY* 1.3 76.7 - - - -
119A VAL* 1.3 62.8 + - - +
189A THR* 6.1 2.2 - - - -
190A MET 3.3 8.7 - - - -
191A GLU* 3.5 36.8 - - + +
192A PHE* 3.6 2.8 - - - -
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Residues in contact with VAL 119 (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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102A TYR* 3.9 28.3 - - + -
103A ASP 3.3 10.8 - - - +
104A LEU* 4.1 15.5 - - + -
118A THR* 1.3 76.3 - - - +
120A SER* 1.3 64.9 + - - +
121A ILE* 4.0 10.3 - - + -
188A LEU 3.4 1.9 - - - +
189A THR* 2.9 24.3 - - - -
190A MET* 3.0 35.2 + - + -
192A PHE* 4.0 15.9 - - + -
231A PHE* 4.7 0.9 - - + -
232A PRO* 3.9 21.3 - - + +
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Residues in contact with SER 120 (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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101A HIS* 3.6 1.4 + - - +
102A TYR* 3.4 3.1 - - - -
103A ASP* 2.7 56.1 + - - +
119A VAL* 1.3 71.7 - - - +
121A ILE* 1.3 60.7 + - - +
187A LEU* 4.3 17.1 - - - +
188A LEU 3.3 4.5 - - - -
189A THR* 2.9 26.8 - - - +
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Residues in contact with ILE 121 (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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99A PRO* 4.0 17.9 - - + -
101A HIS 3.3 9.0 - - - +
102A TYR* 3.8 39.9 - - + -
119A VAL* 4.0 11.9 - - + -
120A SER* 1.3 76.8 - - - +
122A SER* 1.3 61.5 + - - +
123A ILE* 3.7 10.9 + - + +
134A LEU* 3.5 32.8 - - + -
186A TYR 3.6 0.3 - - - +
187A LEU* 3.4 6.7 - - - +
188A LEU* 2.8 48.0 + - + +
190A MET* 4.8 2.2 - - - -
232A PRO 4.2 7.0 - - - +
234A PHE* 4.1 9.6 - - + -
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Residues in contact with SER 122 (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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99A PRO* 3.4 4.5 - - - +
100A VAL* 2.7 40.7 + - - +
101A HIS* 2.8 47.2 + - - +
121A ILE* 1.3 71.3 - - - +
123A ILE* 1.3 56.9 + - - +
185A LEU* 3.8 20.2 - - - +
186A TYR 3.2 8.1 - - - -
187A LEU* 3.7 13.4 - - - +
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Residues in contact with ILE 123 (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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97A VAL* 3.5 27.6 - - + -
98A ASN 3.3 6.5 - - - +
99A PRO* 4.8 0.2 - - + -
121A ILE* 3.8 9.6 - - + +
122A SER* 1.3 77.7 - - - +
124A ASN* 1.3 66.3 + - - +
125A LEU* 3.5 10.4 + - + +
132A LEU* 4.5 16.4 - - + -
147A LEU* 5.5 0.9 - - + -
180A SER* 4.5 0.3 + - - -
185A LEU* 3.9 5.9 - - - +
186A TYR* 2.8 43.5 + - + +
188A LEU* 3.9 35.4 - - + +
234A PHE* 3.8 31.4 - - + -
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Residues in contact with ASN 124 (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 PHE 3.2 6.4 - - - +
98A ASN* 2.6 46.1 + - + +
100A VAL* 4.4 9.5 - - + +
122A SER 4.2 0.2 + - - -
123A ILE* 1.3 69.4 - - - +
125A LEU* 1.3 63.2 + - - +
126A SER* 4.0 10.0 + - - -
180A SER* 3.1 23.7 + - - +
182A GLY 5.4 4.8 + - - -
185A LEU* 3.6 20.8 - - + +
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Residues in contact with LEU 125 (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 PHE* 3.4 4.9 - - + +
97A VAL* 4.8 7.0 - - + +
123A ILE* 3.5 8.6 + - + +
124A ASN* 1.3 75.3 - - - +
126A SER* 1.3 59.2 + - - +
127A ALA 2.9 29.8 - - - +
129A THR* 3.7 22.9 - - + -
132A LEU* 4.2 18.6 - - + -
177A LEU* 3.9 7.0 - - + +
178A THR 3.7 4.9 - - - -
179A PRO* 3.3 26.2 - - - +
180A SER* 2.9 30.5 + - - +
186A TYR* 4.0 35.4 - - + -
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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