Contacts of the strand formed by residues 110 - 120 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C ARG 3.5 3.4 + - - -
109C LYS* 1.3 76.5 - - - +
111C ILE* 1.3 66.2 + - - -
112C TYR* 3.5 7.2 - - - -
160C GLN* 3.5 3.8 - - - +
161C MET 3.0 31.4 + - - +
189C LEU* 3.9 5.6 - - - -
191C PHE 3.5 11.0 - - - -
192C PRO* 3.7 2.7 - - - -
193C LEU* 3.7 13.7 - - - +
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 4.4 13.5 - - + -
91A VAL* 4.0 20.2 - - + -
93A ILE* 4.1 11.0 - - + -
110C GLY* 1.3 72.0 - - - -
112C TYR* 1.3 63.7 + - - +
158C LEU* 4.2 24.7 - - + -
159C ILE 3.7 2.5 - - - +
160C GLN* 3.7 30.5 - - + +
189C LEU* 3.6 2.1 - - - +
190C VAL* 2.8 37.7 + - + +
191C PHE* 2.9 42.4 + - + +
193C LEU* 4.0 13.7 - - + -
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Residues in contact with TYR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 4.4 3.8 - - + -
104C PHE* 3.6 31.6 - + - -
106C ALA* 3.8 5.4 - - + -
107C PRO* 3.4 17.5 - - - +
108C ARG* 2.8 38.8 + - - +
110C GLY 3.5 17.3 - - - -
111C ILE* 1.3 74.7 - - - +
113C SER* 1.3 60.2 + - - +
114C PHE* 3.6 23.0 - + + -
157C VAL 3.8 0.5 - - - +
158C LEU* 3.3 8.0 - - - +
159C ILE 3.0 32.8 + - - +
161C MET* 3.7 25.8 - - + -
188C PHE 3.4 5.6 - - - +
189C LEU* 3.7 39.5 - - + +
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 5.2 4.1 - - - -
112C TYR* 1.3 73.9 - - - +
114C PHE* 1.3 68.1 + - - +
115C ASN* 3.6 17.0 + - - -
157C VAL 3.7 1.7 + - - -
158C LEU* 3.4 23.7 - - - +
187C GLY* 3.0 24.8 - - - -
188C PHE* 2.9 43.7 + - - -
190C VAL* 3.9 3.0 - - - +
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE* 3.7 24.5 - + - -
104C PHE* 3.8 9.9 - + - -
112C TYR* 3.6 25.4 - + + -
113C SER* 1.3 79.9 + - - +
115C ASN* 1.3 71.6 + - - +
116C PHE* 5.6 0.9 - - + -
131C LEU* 3.8 24.2 - - + -
156C GLY* 3.2 2.1 - - - -
157C VAL 3.0 33.9 + - - +
159C ILE* 3.6 34.8 - - + -
161C MET* 3.6 13.7 - - - -
167C ALA* 3.6 26.9 - - + -
185C PHE* 4.0 22.9 - + + -
186C SER 3.5 7.0 - - - -
187C GLY* 4.3 0.7 - - - -
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Residues in contact with ASN 115 (chain C).
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* 5.2 11.2 + - - +
117A HIS* 5.5 2.6 + - - -
115B ASN* 4.9 15.6 + - - +
156B GLY* 5.7 4.5 - - - +
113C SER* 3.6 15.8 + - - -
114C PHE* 1.3 86.1 + - - +
116C PHE* 1.3 63.8 + - - +
117C HIS* 5.0 11.6 + - + +
155C ASN 3.7 5.7 - - - +
156C GLY* 3.8 12.0 - - - -
184C THR* 4.7 0.6 - - - -
185C PHE* 3.3 5.1 - - - -
186C SER* 3.0 46.5 + - - +
187C GLY* 6.0 0.2 - - - -
188C PHE* 5.5 3.8 - - - -
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Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE 5.6 0.4 - - - -
115C ASN* 1.3 79.8 - - - +
117C HIS* 1.3 69.1 + - - +
118C VAL* 4.2 3.8 - - + -
129C VAL* 3.7 37.0 - - + -
131C LEU* 4.1 20.6 - - + -
139C ILE* 3.9 22.4 - - + -
141C ALA* 4.1 11.2 - - + -
153C ALA 3.6 19.7 - - - -
154C SER* 3.3 16.5 - - - -
155C ASN* 3.3 33.5 + - + +
156C GLY* 5.3 0.2 - - - -
169C LEU* 3.6 34.3 - - + -
184C THR 3.2 8.5 - - - +
185C PHE* 3.9 4.5 - + + -
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Residues in contact with HIS 117 (chain C).
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* 5.7 4.5 - + - -
115B ASN* 5.5 2.0 + - - -
117B HIS* 5.8 3.8 - + - -
154B SER* 3.5 20.7 + - - +
155B ASN* 3.2 49.2 - - - +
156B GLY* 3.7 8.9 + - - -
115C ASN* 5.0 9.0 + - + +
116C PHE* 1.3 81.7 + - - +
118C VAL* 1.3 62.2 + - - +
119C VAL* 3.8 4.0 - - + -
152C ALA* 4.6 6.7 - - + +
153C ALA 3.8 4.0 - - - -
154C SER* 2.8 30.0 + - - +
155C ASN 5.5 1.2 + - - -
183C SER* 3.0 6.6 - - - -
184C THR* 2.7 46.5 + - - +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ILE* 4.0 22.0 - - + -
86C PHE* 5.0 1.6 - - + -
116C PHE* 4.2 9.0 - - + -
117C HIS* 1.3 73.4 - - - +
119C VAL* 1.3 62.1 + - - +
120C LYS* 3.8 1.2 + - - +
127C ILE* 4.3 6.2 - - + +
129C VAL* 3.8 39.5 - - + -
151C GLU 3.9 0.5 - - - +
152C ALA* 3.3 1.7 - - - -
153C ALA* 3.0 34.2 + - + +
169C LEU* 4.4 9.4 - - + -
176C LEU* 4.2 24.0 - - + -
180C TRP* 4.5 6.1 - - + -
183C SER* 3.4 11.7 - - - +
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B SER 5.3 2.0 - - - +
141B ALA* 6.3 0.7 - - - -
142B PHE* 4.5 13.0 - - + -
155B ASN* 5.3 2.9 - - - +
117C HIS* 4.4 6.5 - - + +
118C VAL* 1.3 73.7 - - - +
120C LYS* 1.3 61.9 + - - +
150C ARG* 3.7 38.6 - - + -
151C GLU 3.7 9.4 - - - +
152C ALA* 4.1 14.4 - - + +
180C TRP* 3.1 29.4 - - - +
181C LYS 3.5 13.0 + - - +
182C TYR* 3.7 26.2 - - + +
183C SER* 2.8 10.5 + - - +
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Residues in contact with LYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL 3.8 0.6 + - - -
119C VAL* 1.3 74.6 - - - +
121C VAL* 1.3 77.0 + - - +
123C ASN* 2.9 33.1 + - - +
125C GLN 2.9 22.6 + - - -
127C ILE* 3.6 41.5 - - + -
143C ALA* 4.1 7.2 - - + +
144C GLY 3.1 23.4 + - - +
145C ASP* 3.5 9.5 + - - +
146C GLN 5.2 0.2 - - - +
150C ARG* 3.5 26.4 - - - +
151C GLU* 3.2 17.7 + - + +
176C LEU* 4.4 11.4 - - + -
179C GLY 4.4 6.3 - - - +
180C TRP* 5.0 0.2 - - - +
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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