Contacts of the strand formed by residues 167 - 176 (chain I) in PDB entry 4EUP
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 PHE 167 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112I ILE* 6.4 1.1 - - + -
114I ASN 5.2 9.4 - - - -
137I ASP* 4.1 15.7 - - - -
160I LEU* 5.7 0.9 - - + -
161I ASP* 3.7 2.0 + - - +
162I MET* 3.1 53.0 + - + +
165I MET* 3.7 22.2 - - + +
166I ASP* 1.3 78.1 - - - +
168I LYS* 1.3 86.8 + - - +
169I SER* 3.7 19.3 - - - -
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Residues in contact with LYS 168 (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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14I GLU* 2.6 39.9 + - - +
80I PRO* 4.1 14.3 - - + +
110I PRO* 4.3 19.7 - - + -
112I ILE* 3.7 16.3 - - + +
159I VAL* 4.7 7.0 - - + -
160I LEU 3.5 15.0 - - - +
161I ASP* 3.3 31.4 + - + +
166I ASP* 4.5 6.3 + - - -
167I PHE* 1.3 96.0 - - - +
169I SER* 1.3 66.0 + - - +
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Residues in contact with SER 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ILE* 4.1 8.9 - - - +
136I THR* 4.1 3.5 + - - -
137I ASP* 3.2 28.8 + - - +
138I PHE 5.6 0.2 - - - -
158I CYS 3.7 1.0 - - - +
159I VAL* 3.8 3.7 - - - +
160I LEU* 3.3 46.7 + - - +
167I PHE* 3.7 14.4 - - - -
168I LYS* 1.3 79.8 - - - +
170I ASN* 1.3 66.1 + - - +
171I SER* 5.2 0.5 + - - -
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Residues in contact with ASN 170 (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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110I PRO* 4.0 5.4 - - - +
112I ILE* 3.8 9.7 - - - +
136I THR* 3.2 4.0 + - - -
137I ASP 3.1 24.2 + - - +
138I PHE* 3.4 46.7 + - + +
140I SER* 3.7 20.8 + - - -
157I LYS* 4.2 18.1 - - + +
158I CYS 3.3 5.5 + - - +
159I VAL* 3.1 33.9 - - - +
169I SER* 1.3 73.8 - - - +
171I SER* 1.3 67.4 + - - +
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Residues in contact with SER 171 (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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134I LEU* 4.0 13.9 - - - -
135I PHE 3.1 12.1 - - - -
136I THR* 3.9 9.6 - - - -
138I PHE* 3.8 6.8 - - - -
155I THR* 5.2 0.3 - - - +
156I ASP 3.7 0.9 - - - +
157I LYS* 3.5 2.6 - - - -
158I CYS* 3.0 42.2 + - - +
160I LEU* 4.4 16.7 - - - +
169I SER* 5.5 1.1 - - - -
170I ASN* 1.3 79.3 - - - +
172I ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 172 (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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134I LEU* 3.6 4.3 - - - +
135I PHE* 2.7 37.7 + - + +
138I PHE* 4.5 0.8 - - - -
144I VAL* 4.1 20.4 - - + -
155I THR* 3.1 27.8 - - - +
156I ASP 4.4 3.6 - - - +
171I SER* 1.3 77.2 - - - +
173I VAL* 1.3 57.6 + - - +
187I PHE* 3.5 18.9 - - + -
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Residues in contact with VAL 173 (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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132I VAL* 3.5 42.8 - - + -
133I CYS 3.2 5.8 - - - +
134I LEU* 4.9 6.3 - - + +
153I TYR 3.9 0.9 - - - +
154I ILE* 3.7 1.4 - - - -
155I THR* 3.2 44.5 + - + +
172I ALA* 1.3 76.1 - - - +
174I ALA* 1.3 64.5 + - - +
175I TRP* 3.8 12.8 - - + -
187I PHE* 4.0 1.5 - - - -
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Residues in contact with ALA 174 (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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132I VAL 3.8 0.3 - - - -
133I CYS* 2.6 42.0 + - + +
152I VAL* 5.2 0.2 - - + -
153I TYR 3.2 10.8 - - - +
154I ILE* 3.6 22.4 - - + -
173I VAL* 1.3 76.2 - - - +
175I TRP* 1.3 63.1 + - - +
181I PHE* 4.1 14.4 - - + -
186I ALA* 4.5 4.5 - - + -
187I PHE* 3.7 17.0 - - + -
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Residues in contact with TRP 175 (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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131I SER 4.3 9.4 - - - +
132I VAL* 4.1 19.3 - - + -
152I VAL* 3.6 3.4 - - - +
153I TYR* 2.8 74.4 + + + -
154I ILE 5.7 0.4 - - - -
155I THR* 4.0 11.9 - - - -
173I VAL* 3.8 34.3 - - + -
174I ALA* 1.3 81.9 - - - +
176I SER* 1.3 69.4 + - - +
177I ASN* 5.9 3.6 - - - -
181I PHE* 4.3 6.5 - - - -
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Residues in contact with SER 176 (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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131I SER 5.2 4.6 + - - +
151I ASP 2.7 26.8 + - - -
152I VAL* 3.8 11.3 - - - +
153I TYR* 4.8 2.9 - - - -
175I TRP* 1.3 84.0 - - - +
177I ASN* 1.3 73.2 + - - +
178I LYS* 3.6 18.8 + - - +
181I PHE* 3.8 32.3 - - - -
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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