Contacts of the strand formed by residues 129 - 139 (chain I) in PDB entry 3KYM
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 129 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124I GLN* 3.5 31.3 + - - +
125I LEU* 3.7 6.5 + - - +
127I SER* 3.8 10.1 + - - -
128I GLY* 1.3 80.8 + - - +
130I ALA* 1.3 64.4 + - - +
180I THR* 4.1 20.2 - - + -
181I LEU 3.7 12.6 - - - +
182I SER* 4.8 0.7 - - - +
183I LYS* 4.1 3.3 - - - +
149J LYS* 4.2 18.8 - - - +
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Residues in contact with ALA 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I PRO* 4.1 9.0 - - + -
124I GLN* 3.3 7.2 - - - +
125I LEU* 3.7 20.4 - - + -
129I THR* 1.3 76.8 - - - +
131I SER* 1.3 59.7 + - - +
132I VAL* 4.3 2.2 - - + +
179I LEU 3.7 0.3 - - - +
180I THR* 3.4 7.8 - - - +
181I LEU* 2.8 43.2 + - + +
182I SER 4.9 0.7 - - - +
186I TYR* 3.8 26.5 - - + -
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Residues in contact with SER 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I PHE 4.1 0.7 - - - +
119I PRO 4.0 1.2 - - - -
120I PRO* 3.2 25.7 - - - +
124I GLN* 3.0 17.5 + - - +
130I ALA* 1.3 74.0 + - - +
132I VAL* 1.3 62.6 + - - +
133I VAL* 4.2 5.1 + - - +
178I THR* 4.0 15.6 - - - +
179I LEU 3.3 9.1 + - - -
180I THR* 4.2 4.2 + - - -
130J LEU* 5.4 3.3 - - - +
147J LEU* 3.9 17.2 - - - +
149J LYS* 3.0 25.8 + - - -
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Residues in contact with VAL 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ILE* 4.0 16.4 - - + -
118I PHE 3.5 14.1 - - - +
119I PRO* 4.2 9.2 - - + -
120I PRO* 4.4 9.9 - - + -
130I ALA 5.3 1.8 - - - -
131I SER* 1.3 79.8 - - - +
133I VAL* 1.3 61.6 + - - +
148I TRP* 3.7 26.9 - - + -
177I SER 3.8 1.0 - - - +
178I THR* 3.5 4.3 - - - +
179I LEU* 2.9 52.0 + - + +
181I LEU* 5.3 3.1 - - + -
186I TYR* 4.9 8.5 - - + -
192I TYR* 4.5 19.5 - - + -
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Residues in contact with VAL 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ILE* 3.5 1.9 - - - +
118I PHE* 2.8 61.9 + - + +
131I SER* 4.9 3.4 - - - -
132I VAL* 1.3 80.9 - - - +
134I CYS* 1.3 68.2 + - - +
135I LEU* 5.4 0.7 - - + -
148I TRP* 4.5 2.2 - - - -
176I SER* 5.0 7.4 - - - -
177I SER 3.8 2.2 - - - -
178I THR* 3.8 24.7 - - + +
130J LEU* 3.8 34.1 - - + -
147J LEU* 4.5 7.6 - - + -
185J SER* 4.3 10.1 - - - +
187J VAL* 5.5 2.2 - - + -
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Residues in contact with CYS 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I VAL* 3.8 15.3 - - - -
116I PHE 3.2 16.4 - - - -
117I ILE* 4.5 1.6 - - - +
133I VAL* 1.3 76.1 - - - +
135I LEU* 1.3 61.1 + - - +
136I LEU* 4.1 6.5 - - + -
146I VAL* 4.9 0.7 - - + -
148I TRP* 3.7 14.3 - - + -
175I LEU 3.7 0.2 - - - +
176I SER* 3.3 9.0 - - - -
177I SER* 3.1 35.2 + - - +
194I CYS* 2.0 51.6 - - + -
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Residues in contact with LEU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I SER 3.2 3.3 - - - +
115I VAL* 3.1 6.8 - - - -
116I PHE* 2.7 44.2 + - + -
118I PHE* 3.7 19.7 - - + -
133I VAL* 4.1 1.3 + - + -
134I CYS* 1.3 74.8 - - - +
136I LEU* 1.3 68.3 + - - +
137I ASN* 3.9 27.8 - - + +
174I SER* 4.9 0.9 - - - -
175I LEU 3.3 16.2 - - - +
176I SER* 4.9 1.3 - - - -
143J ALA* 4.3 21.1 - - + -
172J PHE* 3.9 20.9 - - + -
187J VAL* 3.8 31.4 - - + -
189J THR* 5.2 0.4 - - - -
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Residues in contact with LEU 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I PRO* 4.7 5.4 - - + -
114I SER 3.8 2.5 - - - -
115I VAL* 3.4 21.3 - - + -
134I CYS* 4.5 5.4 - - + -
135I LEU* 1.3 76.2 - - - +
137I ASN* 1.3 58.5 + - - +
139I PHE* 3.1 21.7 - - + -
144I ALA* 4.7 15.0 - - + -
145I LYS 5.4 0.7 - - - +
146I VAL* 4.0 14.4 - - + -
174I SER* 3.4 0.3 - - - -
175I LEU* 2.7 64.9 + - + +
177I SER* 5.8 0.4 - - - +
196I VAL* 3.0 49.4 - - + -
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Residues in contact with ASN 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I ALA 3.7 0.9 - - - +
113I PRO* 3.5 1.1 - - - +
114I SER* 3.0 52.9 + - - +
116I PHE* 4.7 0.9 - - + -
135I LEU* 3.9 22.7 - - + +
136I LEU* 1.3 74.3 - - - +
138I ASN* 1.3 94.0 + - - +
139I PHE* 3.7 3.8 - - - -
174I SER* 3.6 10.4 + - - -
170J HIS* 3.6 8.1 - - - -
187J VAL* 5.2 1.2 - - - +
189J THR* 3.5 33.9 + - - +
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Residues in contact with ASN 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I ALA* 3.6 9.4 - - - +
112I ALA 3.0 17.0 - - - +
137I ASN* 1.3 87.6 + - - +
139I PHE* 1.3 55.6 + - - +
170I ASP* 4.4 9.0 + - - +
172I THR* 3.7 24.0 + - + +
173I TYR 2.9 15.8 + - - -
174I SER* 3.1 14.0 + - - -
170J HIS* 3.2 15.2 + - - -
189J THR* 4.6 8.5 - - - +
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Residues in contact with PHE 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I ALA* 3.9 7.4 - - - +
113I PRO* 3.6 32.5 - - + -
136I LEU* 3.1 44.0 - - + -
137I ASN 3.8 3.1 - - - -
138I ASN* 1.3 73.6 - - - +
140I TYR* 1.3 60.5 + - - +
141I PRO 3.4 19.1 - - - -
142I ARG* 4.4 14.4 - - - -
144I ALA* 4.6 11.7 - - + -
163I VAL* 5.8 1.1 - - + -
172I THR* 3.8 1.5 - - - -
173I TYR* 2.9 50.9 + - + +
174I SER* 3.7 7.9 - - - -
175I LEU* 3.5 33.0 - - + -
198I HIS* 4.1 9.6 - + + +
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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