Contacts of the strand formed by residues 110 - 120 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG 3.5 3.2 + - - -
109B LYS* 1.3 76.1 - - - +
111B ILE* 1.3 64.2 + - - -
112B TYR* 3.5 7.8 - - - -
160B GLN* 3.5 4.0 - - - +
161B MET 3.1 29.9 + - - +
189B LEU* 3.9 5.6 - - - -
191B PHE 3.4 11.7 - - - -
192B PRO* 3.8 2.5 - - - -
193B LEU* 3.8 14.4 - - - -
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLY* 1.3 71.9 - - - -
112B TYR* 1.3 55.7 + - - +
158B LEU* 4.3 22.2 - - + -
159B ILE 3.7 4.0 - - - +
160B GLN* 3.8 29.6 - - + +
189B LEU* 3.6 2.5 - - - +
190B VAL* 2.7 45.7 + - + +
191B PHE* 2.8 43.9 + - + +
193B LEU* 4.1 13.7 - - + -
63C ALA* 4.4 13.0 - - + -
91C VAL* 3.9 20.0 - - + -
93C ILE* 4.1 9.6 - - + -
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.4 4.0 - - + -
104B PHE* 3.6 31.2 - + - -
106B ALA* 3.7 5.3 - - + +
107B PRO* 3.5 16.3 - - - +
108B ARG* 2.7 38.1 + - - +
110B GLY 3.5 18.2 - - - -
111B ILE* 1.3 74.1 - - - +
113B SER* 1.3 59.6 + - - +
114B PHE* 3.7 21.5 - + + -
157B VAL 3.8 0.5 - - - +
158B LEU* 3.4 4.2 - - - +
159B ILE* 2.9 35.5 + - - +
161B MET* 3.8 26.2 - - + -
188B PHE 3.4 6.1 - - - +
189B LEU* 3.6 40.4 - - + +
190B VAL* 4.1 3.6 - - - -
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B TYR* 1.3 74.1 - - - +
114B PHE* 1.3 68.6 + - - +
115B ASN* 3.6 17.2 + - - -
157B VAL 3.6 1.5 + - - -
158B LEU* 3.4 24.0 - - - +
187B GLY* 3.0 23.7 - - - -
188B PHE* 2.9 43.1 + - - -
190B VAL* 3.7 3.0 - - - +
188C PHE* 5.1 3.7 - - - -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.8 23.1 - + - -
104B PHE* 3.8 10.3 - + - -
112B TYR* 3.7 24.5 - + + -
113B SER* 1.3 78.6 + - - +
115B ASN* 1.3 68.9 + - - +
116B PHE* 5.6 1.6 - - + -
131B LEU* 3.8 25.8 - - + -
156B GLY* 3.0 5.5 - - - -
157B VAL 3.0 34.2 + - - +
159B ILE* 3.7 27.6 - - + -
161B MET* 3.6 20.6 - - - -
167B ALA* 3.6 26.2 - - + -
185B PHE* 4.0 20.4 - + + -
186B SER 3.5 7.0 - - - -
187B GLY* 4.1 2.2 - - - -
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Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASN* 4.9 14.8 + - - +
156A GLY* 6.0 2.9 - - - +
113B SER* 3.6 15.0 + - - -
114B PHE* 1.3 86.6 + - - +
116B PHE* 1.3 64.9 + - - +
117B HIS* 5.0 12.7 + - + +
155B ASN 3.7 5.9 - - - +
156B GLY* 3.7 12.5 - - - -
184B THR* 4.6 0.4 - - - -
185B PHE* 3.5 2.5 - - - -
186B SER* 2.8 47.3 + - - +
187B GLY* 6.1 0.4 - - - -
188B PHE* 5.4 4.6 - - - -
115C ASN* 4.9 15.1 - - - +
117C HIS* 5.5 1.6 + - - -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE 5.6 0.4 - - - -
115B ASN* 1.3 80.2 - - - +
117B HIS* 1.3 69.1 + - - +
118B VAL* 4.1 11.7 - - + -
129B VAL* 3.7 30.7 - - + -
131B LEU* 4.1 17.9 - - + -
139B ILE* 4.0 22.2 - - + -
141B ALA* 3.9 12.6 - - + -
153B ALA 3.4 20.2 - - - -
154B SER* 3.3 2.8 - - - -
155B ASN* 3.2 48.7 + - + +
156B GLY* 5.4 0.2 - - - -
169B LEU* 3.5 29.8 - - + -
184B THR 3.1 13.0 - - - +
185B PHE* 4.0 4.3 - + + -
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Residues in contact with HIS 117 (chain B).
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* 5.0 4.0 + - - -
117A HIS* 5.5 5.2 - + - -
154A SER* 3.5 21.7 + - - +
155A ASN* 3.3 42.3 - - - +
156A GLY* 3.7 14.6 + - - -
115B ASN* 5.0 10.6 + - + +
116B PHE* 1.3 84.8 + - - +
118B VAL* 1.3 62.4 + - - +
119B VAL* 3.8 3.1 - - + +
152B ALA* 5.0 4.9 - - + -
153B ALA 3.8 3.8 - - - -
154B SER* 3.0 29.6 + - - +
155B ASN 5.5 1.7 + - - -
183B SER* 3.1 6.1 - - - -
184B THR* 2.7 47.4 + - - +
117C HIS* 5.8 4.0 - + - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE* 3.9 13.7 - - + -
86B PHE* 5.0 1.8 - - + -
116B PHE* 4.1 9.9 - - + -
117B HIS* 1.3 72.6 - - - +
119B VAL* 1.3 63.2 + - - +
120B LYS 3.8 0.3 + - - -
127B ILE* 4.4 6.2 - - + +
129B VAL* 3.8 43.1 - - + -
151B GLU 3.5 1.2 - - - +
152B ALA* 3.3 4.2 - - - +
153B ALA* 3.0 31.5 + - + +
169B LEU* 4.5 7.9 - - + -
176B LEU* 4.2 31.4 - - + -
180B TRP* 4.6 4.0 - - + -
183B SER* 3.4 10.3 - - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER 4.9 3.4 - - - +
141A ALA* 6.0 0.7 - - - -
142A PHE* 4.3 11.7 - - + -
155A ASN* 4.9 7.0 - - - +
117B HIS* 4.3 4.5 - - + +
118B VAL* 1.3 73.0 - - - +
120B LYS* 1.3 61.4 + - - +
150B ARG* 3.5 39.7 + - + -
151B GLU 3.5 7.2 - - - +
152B ALA* 4.6 11.4 - - + -
180B TRP* 3.0 30.1 - - - +
181B LYS 3.4 14.0 - - - +
182B TYR* 3.7 26.5 - - + +
183B SER* 2.7 10.3 + - - +
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL 3.8 0.4 + - - -
119B VAL* 1.3 74.0 - - - +
121B VAL* 1.3 86.0 + - - +
122B TYR* 5.1 0.2 - - - +
123B ASN* 2.6 19.9 + - - +
125B GLN 2.3 34.1 + - - -
126B THR* 4.1 1.2 - - - +
127B ILE* 3.7 40.2 - - + +
143B ALA* 4.1 3.6 - - + -
144B GLY 3.8 21.8 + - - +
145B ASP* 4.3 3.7 + - - +
146B GLN 5.9 0.4 - - - +
150B ARG* 3.2 29.5 - - - +
151B GLU* 3.0 24.3 + - + +
176B LEU* 4.3 12.1 - - + -
179B GLY 4.4 5.4 - - - +
180B TRP* 4.9 0.4 - - - +
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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
------------------------------------------------------------
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