Contacts of the strand formed by residues 110 - 120 (chain A) in PDB entry 5KC6
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 GLY 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG 3.5 3.2 + - - -
109A LYS* 1.3 76.3 - - - +
111A ILE* 1.3 65.2 + - - -
112A TYR* 3.5 6.7 - - - -
160A GLN* 3.5 3.6 - - - +
161A MET 3.0 30.5 + - - +
189A LEU* 4.0 5.6 - - - -
191A PHE 3.5 11.9 - - - -
192A PRO* 3.7 3.1 - - - -
193A LEU* 3.7 13.2 - - - -
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Residues in contact with ILE 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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110A GLY* 1.3 71.9 - - - -
112A TYR* 1.3 62.9 + - - +
158A LEU* 4.3 22.0 - - + -
159A ILE 3.6 4.0 - - - +
160A GLN* 3.6 30.1 - - + +
189A LEU* 3.5 3.5 - - - +
190A VAL* 2.8 38.7 + - + +
191A PHE* 2.9 41.8 + - + +
193A LEU* 3.9 14.4 - - + -
63B ALA* 4.6 8.5 - - + -
91B VAL* 3.9 25.1 - - + -
93B ILE* 4.1 9.2 - - + -
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Residues in contact with TYR 112 (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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62A VAL* 4.4 2.0 - - + -
104A PHE* 3.7 32.8 - + - -
106A ALA* 3.9 6.1 - - + -
107A PRO* 3.4 18.3 - - + +
108A ARG* 2.7 38.1 + - - +
110A GLY 3.5 19.3 - - - -
111A ILE* 1.3 75.8 - - - +
113A SER* 1.3 60.7 + - - +
114A PHE* 3.5 21.5 - + + -
157A VAL 3.9 0.9 - - - +
158A LEU* 3.3 5.3 - - - +
159A ILE* 2.9 34.2 + - - +
161A MET* 3.7 26.7 - - + -
188A PHE 3.5 3.8 - - - +
189A LEU* 3.6 40.6 - - + +
190A VAL* 4.2 2.5 - - - -
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Residues in contact with SER 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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112A TYR* 1.3 73.6 - - - +
114A PHE* 1.3 68.3 + - - +
115A ASN* 3.6 16.3 + - - -
157A VAL 3.7 0.7 + - - -
158A LEU* 3.4 25.1 - - - +
187A GLY* 3.0 24.2 - - - -
188A PHE* 2.9 44.1 + - - +
190A VAL* 3.9 4.8 - - - +
188B PHE* 5.2 3.1 - - - -
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Residues in contact with PHE 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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64A PHE* 3.7 27.8 - + - -
104A PHE* 3.8 13.9 - + - -
112A TYR* 3.5 25.8 - - + -
113A SER* 1.3 80.5 + - - +
115A ASN* 1.3 69.3 + - - +
116A PHE* 5.8 1.1 - - + -
131A LEU* 3.9 23.8 - - + -
156A GLY* 3.1 4.8 - - - -
157A VAL 3.0 34.7 + - - +
159A ILE* 3.8 25.6 - - + -
161A MET* 3.6 27.1 - - - -
167A ALA* 3.8 17.7 - - + -
185A PHE* 4.1 21.5 - + + -
186A SER 3.6 3.4 - - - -
187A GLY 5.3 0.4 - - - -
188A PHE 5.8 0.2 - - - -
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Residues in contact with ASN 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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113A SER* 3.6 15.8 + - - -
114A PHE* 1.3 85.8 + - - +
116A PHE* 1.3 62.9 + - - +
117A HIS* 5.1 10.9 + - + +
155A ASN 3.7 6.9 - - - +
156A GLY* 3.8 11.4 - - - -
184A THR* 4.7 0.4 - - - -
185A PHE* 3.3 4.8 - - - -
186A SER* 2.9 46.2 + - - +
187A GLY* 6.0 0.6 - - - -
188A PHE* 5.5 3.8 - - - -
115B ASN* 4.9 15.6 - - - +
117B HIS* 5.0 4.2 + - - -
115C ASN* 5.2 10.5 + - - +
156C GLY* 6.0 3.4 - - - +
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Residues in contact with PHE 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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114A PHE 5.8 0.7 - - - -
115A ASN* 1.3 79.1 - - - +
117A HIS* 1.3 69.2 + - - +
118A VAL* 4.1 5.8 - - + -
129A VAL* 3.7 36.6 - - + -
131A LEU* 4.2 17.3 - - + -
139A ILE* 3.9 21.5 - - + -
140A SER 4.7 1.6 - - - -
141A ALA* 3.9 14.6 - - + -
153A ALA 3.4 20.0 - - - -
154A SER* 3.3 15.9 - - - -
155A ASN* 3.1 34.2 + - + +
156A GLY* 5.3 0.2 - - - -
169A LEU* 3.6 30.3 - - + -
184A THR 3.2 12.1 - - - +
185A PHE* 3.9 5.8 - + + -
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Residues in contact with HIS 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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115A ASN* 5.1 9.4 + - + +
116A PHE* 1.3 81.8 + - - +
118A VAL* 1.3 62.9 + - - +
119A VAL* 3.9 2.7 - - + -
152A ALA* 4.6 6.7 - - + +
153A ALA 3.8 3.4 - - - -
154A SER* 2.9 31.3 + - - +
155A ASN 5.7 0.4 + - - -
183A SER* 3.0 6.6 - - - -
184A THR* 2.6 47.9 + - - +
117B HIS* 5.5 5.6 - + - -
115C ASN* 5.5 2.4 + - - -
117C HIS* 5.7 3.8 - + - -
154C SER* 3.5 20.9 + - - +
155C ASN* 3.3 48.5 - - - +
156C GLY* 3.8 9.0 + - - -
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Residues in contact with VAL 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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84A ILE* 4.0 14.8 - - + -
86A PHE* 4.8 1.1 - - + -
116A PHE* 4.1 9.0 - - + -
117A HIS* 1.3 72.2 - - - +
119A VAL* 1.3 64.1 + - - +
120A LYS 3.8 1.4 + - - -
127A ILE* 4.3 5.8 - - + +
129A VAL* 3.8 43.3 - - + -
151A GLU 3.9 0.2 - - - +
152A ALA* 3.3 1.4 - - - -
153A ALA* 2.9 36.4 + - + +
169A LEU* 4.3 9.6 - - + -
176A LEU* 4.2 31.9 - - + -
180A TRP* 4.5 1.3 - - + -
183A SER* 3.4 11.2 - - - +
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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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117A HIS* 4.4 6.3 - - + +
118A VAL* 1.3 73.4 - - - +
120A LYS* 1.3 62.4 + - - +
150A ARG* 3.7 40.2 + - + -
151A GLU 3.7 9.0 - - - +
152A ALA* 4.0 13.7 - - + +
180A TRP* 3.1 28.6 - - - +
181A LYS 3.5 13.5 - - - +
182A TYR* 3.6 26.5 - - + +
183A SER* 2.8 10.3 + - - +
140C SER 5.1 4.9 - - - +
141C ALA* 6.2 0.7 - - - -
142C PHE* 4.4 11.9 - - + -
155C ASN* 5.2 1.6 - - - +
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Residues in contact with LYS 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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118A VAL 3.8 0.8 + - - -
119A VAL* 1.3 75.6 - - - +
121A VAL* 1.3 73.1 + - - +
123A ASN* 2.7 21.2 + - - +
125A GLN 2.1 35.0 + - - -
126A THR* 4.2 0.4 - - - +
127A ILE* 3.8 34.1 - - + +
143A ALA* 4.4 5.8 - - + -
144A GLY 3.2 24.8 + - - -
145A ASP* 3.6 9.0 + - - -
146A GLN 5.8 0.2 - - - +
150A ARG* 3.6 26.0 - - - +
151A GLU* 3.2 17.1 + - + +
176A LEU* 4.0 20.4 - - + -
177A MET 6.1 0.2 - - - +
179A GLY 4.4 6.3 - - - +
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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