Contacts of the strand formed by residues 124 - 130 (chain A) in PDB entry 3L2Q
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 LYS 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PRO* 4.2 23.6 - - + +
120A LYS 4.8 0.2 + - - -
122A PHE 3.3 0.6 - - - -
123A ASP* 1.3 81.7 - - + +
125A PHE* 1.3 74.2 + - - +
126A PHE* 3.6 30.8 - - + -
147A ASP* 3.4 8.0 + - - +
148A GLY 2.8 27.3 + - - -
181A VAL* 3.1 27.1 - - + +
183A HIS* 4.5 3.3 + - + -
207A GLU* 2.8 38.0 + - - +
3C T 3.9 18.6 + - - +
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Residues in contact with PHE 125 (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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122A PHE* 3.8 33.7 - + - -
124A LYS* 1.3 81.0 - - - +
126A PHE* 1.3 59.0 + - - +
127A ILE* 4.7 2.2 - - + -
145A VAL* 3.7 26.0 - - + -
146A VAL 3.5 1.6 - - - -
147A ASP* 3.9 29.2 - - + -
154A TRP* 4.0 17.0 - + - -
170A LEU* 5.2 3.4 - - + -
173A LEU* 4.2 18.8 - - + -
174A THR* 5.3 2.9 - - + -
177A ALA 5.3 2.5 - - - -
179A PRO* 3.8 31.2 - - + -
181A VAL 2.7 7.9 + - - -
182A ILE* 3.7 21.5 - - + +
183A HIS* 2.6 36.4 + - - +
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Residues in contact with PHE 126 (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 PRO* 5.0 4.9 - - + -
124A LYS* 3.6 26.2 - - + -
125A PHE* 1.3 72.3 - - - +
127A ILE* 1.3 63.9 + - - +
144A VAL 3.8 0.3 - - - +
145A VAL* 3.4 0.5 - - - -
146A VAL* 2.8 42.0 + - + +
148A GLY* 4.0 26.2 - - - -
183A HIS* 3.4 43.7 - + + -
216A SER 4.2 13.2 - - - -
217A SER* 4.7 3.4 - - - -
219A LYS* 4.0 27.8 - - + -
220A VAL* 3.1 29.2 - - + +
5C T 5.9 2.2 - - - -
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Residues in contact with ILE 127 (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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125A PHE* 4.7 2.7 - - + -
126A PHE* 1.3 80.9 - - - +
128A ASP* 1.3 67.1 + - - +
143A LEU* 4.7 5.2 - - + -
144A VAL 3.2 4.9 - - - +
145A VAL* 3.7 32.8 - - + -
166A THR* 4.6 7.0 - - + -
170A LEU* 4.8 9.6 - - + -
182A ILE* 3.8 28.0 - - + -
183A HIS 3.1 8.3 + - - +
184A SER* 3.8 25.5 - - - -
185A ASP* 4.4 2.4 - - - +
190A PHE* 3.6 37.3 - - + -
195A PHE* 4.4 10.1 - - + -
217A SER* 5.3 2.1 + - - -
220A VAL* 3.5 5.0 - - - +
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Residues in contact with ASP 128 (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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127A ILE* 1.3 78.2 - - - +
129A TYR* 1.3 77.0 + - - +
143A LEU* 3.7 3.5 - - - +
144A VAL* 2.8 33.8 + - - +
185A ASP* 2.8 22.0 - - - +
190A PHE* 4.6 6.2 - - - -
217A SER* 5.8 0.9 - - - -
220A VAL* 3.5 21.5 - - + -
221A GLU* 2.7 27.0 - - - +
224A ASN* 2.8 19.6 + - - +
17D A 4.1 5.7 + - - +
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Residues in contact with TYR 129 (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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128A ASP* 1.3 88.3 + - - +
130A ILE* 1.3 63.8 + - - +
131A GLY 4.1 1.2 + - - +
141A TYR* 4.0 13.5 - - + -
142A VAL 3.4 13.9 - - - -
143A LEU* 3.6 29.9 - - + +
158A THR* 3.4 23.9 - - + +
160A ALA 3.9 4.7 + - - -
161A PRO* 3.8 35.9 - - + -
162A SER 3.5 3.3 + - - -
165A ALA 3.9 3.1 - - - -
166A THR* 2.7 44.0 + - - -
189A ALA* 4.4 2.5 - - + -
190A PHE* 3.8 21.0 - + - -
224A ASN* 4.9 0.2 + - - -
17D A 5.1 4.2 + - - +
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Residues in contact with ILE 130 (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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128A ASP 4.2 0.4 + - - -
129A TYR* 1.3 72.5 - - - +
131A GLY* 1.3 61.8 + - - +
133A LEU* 3.7 28.9 - - + -
140A LEU 4.4 0.2 - - - +
141A TYR* 3.2 14.2 - - - +
142A VAL* 2.9 38.2 + - + +
144A VAL* 4.2 11.4 - - + +
224A ASN* 3.4 56.8 - - + +
227A ILE* 4.4 13.2 - - + -
228A LYS* 3.8 23.3 - - + -
17D A 4.2 9.9 - - - +
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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